8H2U

X-ray Structure of photosystem I-LHCI super complex from Chlamydomonas reinhardtii.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.359 
  • R-Value Work: 0.291 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Three structures of PSI-LHCI from Chlamydomonas reinhardtii suggest a resting state re-activated by ferredoxin.

Gerle, C.Misumi, Y.Kawamoto, A.Tanaka, H.Kubota-Kawai, H.Tokutsu, R.Kim, E.Chorev, D.Abe, K.Robinson, C.V.Mitsuoka, K.Minagawa, J.Kurisu, G.

(2023) Biochim Biophys Acta Bioenerg 1864: 148986-148986

  • DOI: https://doi.org/10.1016/j.bbabio.2023.148986
  • Primary Citation of Related Structures:  
    7WYI, 7WZN, 8H2U

  • PubMed Abstract: 

    Photosystem I (PSI) from the green alga Chlamydomonas reinhardtii, with various numbers of membrane bound antenna complexes (LHCI), has been described in great detail. In contrast, structural characterization of soluble binding partners is less advanced. Here, we used X-ray crystallography and single particle cryo-EM to investigate three structures of the PSI-LHCI supercomplex from Chlamydomonas reinhardtii. An X-ray structure demonstrates the absence of six chlorophylls from the luminal side of the LHCI belts, suggesting these pigments were either physically absent or less stably associated with the complex, potentially influencing excitation transfer significantly. CryoEM revealed extra densities on luminal and stromal sides of the supercomplex, situated in the vicinity of the electron transfer sites. These densities disappeared after the binding of oxidized ferredoxin to PSI-LHCI. Based on these structures, we propose the existence of a PSI-LHCI resting state with a reduced active chlorophyll content, electron donors docked in waiting positions and regulatory binding partners positioned at the electron acceptor site. The resting state PSI-LHCI supercomplex would be recruited to its active form by the availability of oxidized ferredoxin.


  • Organizational Affiliation

    Life Science Research Infrastructure Group, RIKEN SPring-8 Center, Kouto, Hyogo, Japan; Laboratory for Protein Crystallography, Institute for Protein Research, Osaka University, Suita, Osaka, Japan. Electronic address: christoph.gerle@riken.jp.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1751Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P12154 (Chlamydomonas reinhardtii)
Explore P12154 
Go to UniProtKB:  P12154
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12154
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2735Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P09144 (Chlamydomonas reinhardtii)
Explore P09144 
Go to UniProtKB:  P09144
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09144
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center81Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for Q00914 (Chlamydomonas reinhardtii)
Explore Q00914 
Go to UniProtKB:  Q00914
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00914
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II, chloroplastic196Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q39615 (Chlamydomonas reinhardtii)
Explore Q39615 
Go to UniProtKB:  Q39615
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ39615
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV, chloroplastic97Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12352 (Chlamydomonas reinhardtii)
Explore P12352 
Go to UniProtKB:  P12352
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12352
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III, chloroplastic227Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12356 (Chlamydomonas reinhardtii)
Explore P12356 
Go to UniProtKB:  P12356
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12356
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit V, chloroplastic126Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P14224 (Chlamydomonas reinhardtii)
Explore P14224 
Go to UniProtKB:  P14224
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14224
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VI, chloroplastic130Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P13352 (Chlamydomonas reinhardtii)
Explore P13352 
Go to UniProtKB:  P13352
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13352
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIII106Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A8IFG7 (Chlamydomonas reinhardtii)
Explore A8IFG7 
Go to UniProtKB:  A8IFG7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8IFG7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IX41Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P59777 (Chlamydomonas reinhardtii)
Explore P59777 
Go to UniProtKB:  P59777
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59777
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit psaK, chloroplastic113Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P14225 (Chlamydomonas reinhardtii)
Explore P14225 
Go to UniProtKB:  P14225
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14225
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
PSI subunit V196Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A8IL32 (Chlamydomonas reinhardtii)
Explore A8IL32 
Go to UniProtKB:  A8IL32
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8IL32
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticM [auth 0],
Q [auth 1]
228Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for Q05093 (Chlamydomonas reinhardtii)
Explore Q05093 
Go to UniProtKB:  Q05093
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05093
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticN [auth 8]243Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for Q75VY7 (Chlamydomonas reinhardtii)
Explore Q75VY7 
Go to UniProtKB:  Q75VY7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ75VY7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticO [auth 7]241Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for Q75VY4 (Chlamydomonas reinhardtii)
Explore Q75VY4 
Go to UniProtKB:  Q75VY4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ75VY4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Lhca3P [auth 3]298Chlamydomonas reinhardtiiMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticR [auth 4]264Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q75VZ0 (Chlamydomonas reinhardtii)
Explore Q75VZ0 
Go to UniProtKB:  Q75VZ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ75VZ0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticS [auth 6]257Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for Q75VY6 (Chlamydomonas reinhardtii)
Explore Q75VY6 
Go to UniProtKB:  Q75VY6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ75VY6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticT [auth 5]257Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for Q75VY8 (Chlamydomonas reinhardtii)
Explore Q75VY8 
Go to UniProtKB:  Q75VY8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ75VY8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

Download Ideal Coordinates CCD File 
GK [auth 5],
PD [auth B]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL (Subject of Investigation/LOI)
Query on CHL

Download Ideal Coordinates CCD File 
AK [auth 5]
BK [auth 5]
DF [auth 0]
DK [auth 5]
EF [auth 0]
AK [auth 5],
BK [auth 5],
DF [auth 0],
DK [auth 5],
EF [auth 0],
EK [auth 5],
FH [auth 3],
GF [auth 0],
GJ [auth 6],
HJ [auth 6],
JJ [auth 6],
KJ [auth 6],
MG [auth 7],
NG [auth 7],
NI [auth 4],
OI [auth 4],
PG [auth 7],
QI [auth 4],
RG [auth 7],
RI [auth 4],
VF [auth 8],
WF [auth 8],
WH [auth 1],
XH [auth 1],
YF [auth 8],
ZH [auth 1]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA (Subject of Investigation/LOI)
Query on CLA

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth A]
AC [auth B]
AD [auth B]
AE [auth G]
AA [auth A],
AB [auth A],
AC [auth B],
AD [auth B],
AE [auth G],
AF [auth 0],
AH [auth 3],
AJ [auth 6],
BA [auth A],
BB [auth A],
BC [auth B],
BD [auth B],
BE [auth G],
BF [auth 0],
BH [auth 3],
BI [auth 1],
BJ [auth 6],
CA [auth A],
CB [auth A],
CC [auth B],
CD [auth B],
CF [auth 0],
CH [auth 3],
CJ [auth 6],
CK [auth 5],
DA [auth A],
DB [auth A],
DC [auth B],
DD [auth B],
DH [auth 3],
DJ [auth 6],
EA [auth A],
EB [auth A],
EC [auth B],
ED [auth B],
EG [auth 7],
EH [auth 3],
EJ [auth 6],
FA [auth A],
FB [auth A],
FC [auth B],
FD [auth B],
FF [auth 0],
FG [auth 7],
FI [auth 4],
FJ [auth 6],
FK [auth 5],
GA [auth A],
GB [auth A],
GC [auth B],
GD [auth B],
GG [auth 7],
GH [auth 3],
GI [auth 4],
HA [auth A],
HB [auth A],
HC [auth B],
HD [auth B],
HE [auth J],
HG [auth 7],
HH [auth 3],
HI [auth 4],
IA [auth A],
IC [auth B],
ID [auth B],
IG [auth 7],
IH [auth 3],
II [auth 4],
IJ [auth 6],
IK [auth 5],
JA [auth A],
JC [auth B],
JG [auth 7],
JI [auth 4],
JK [auth 5],
KA [auth A],
KC [auth B],
KE [auth K],
KG [auth 7],
KI [auth 4],
KK [auth 5],
LA [auth A],
LC [auth B],
LE [auth K],
LG [auth 7],
LI [auth 4],
LJ [auth 6],
MA [auth A],
MC [auth B],
ME [auth L],
MF [auth 8],
MI [auth 4],
NA [auth A],
NC [auth B],
NE [auth L],
NF [auth 8],
NH [auth 1],
NJ [auth 6],
OA [auth A],
OC [auth B],
OE [auth L],
OF [auth 8],
OG [auth 7],
OH [auth 1],
OJ [auth 5],
PA [auth A],
PC [auth B],
PE [auth L],
PF [auth 8],
PH [auth 1],
PI [auth 4],
QA [auth A],
QC [auth B],
QE [auth 0],
QF [auth 8],
QH [auth 1],
RA [auth A],
RC [auth B],
RD [auth B],
RF [auth 8],
RH [auth 1],
RJ [auth 5],
SA [auth A],
SB [auth A],
SC [auth B],
SF [auth 8],
SH [auth 1],
SJ [auth 5],
TA [auth A],
TB [auth A],
TC [auth B],
TF [auth 8],
TH [auth 1],
TJ [auth 5],
U [auth A],
UA [auth A],
UB [auth B],
UC [auth B],
UE [auth 0],
UF [auth 8],
UH [auth 1],
UI [auth 6],
UJ [auth 5],
V [auth A],
VA [auth A],
VB [auth B],
VC [auth B],
VD [auth F],
VE [auth 0],
VH [auth 1],
VJ [auth 5],
W [auth A],
WA [auth A],
WB [auth B],
WC [auth B],
WD [auth F],
WE [auth 0],
WG [auth 3],
WJ [auth 5],
X [auth A],
XA [auth A],
XC [auth B],
XE [auth 0],
XF [auth 8],
XG [auth 3],
XJ [auth 5],
Y [auth A],
YA [auth A],
YB [auth B],
YC [auth B],
YD [auth F],
YE [auth 0],
YG [auth 3],
YH [auth 1],
YI [auth 6],
YJ [auth 5],
Z [auth A],
ZA [auth A],
ZB [auth B],
ZC [auth B],
ZD [auth G],
ZE [auth 0],
ZG [auth 3],
ZI [auth 6],
ZJ [auth 5]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG (Subject of Investigation/LOI)
Query on LMG

Download Ideal Coordinates CCD File 
AG [auth 8]
GE [auth J]
LK [auth 5]
MJ [auth 6]
SE [auth 0]
AG [auth 8],
GE [auth J],
LK [auth 5],
MJ [auth 6],
SE [auth 0],
TI [auth 4],
ZF [auth 8]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG (Subject of Investigation/LOI)
Query on LHG

Download Ideal Coordinates CCD File 
CI [auth 4]
IF [auth 8]
KB [auth A]
KH [auth 3]
QB [auth A]
CI [auth 4],
IF [auth 8],
KB [auth A],
KH [auth 3],
QB [auth A],
QG [auth 7],
RE [auth 0]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
XAT (Subject of Investigation/LOI)
Query on XAT

Download Ideal Coordinates CCD File 
CG [auth 7],
EI [auth 4],
LF [auth 8],
QJ [auth 5],
XI [auth 6]
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O4
SZCBXWMUOPQSOX-WVJDLNGLSA-N
LUT (Subject of Investigation/LOI)
Query on LUT

Download Ideal Coordinates CCD File 
AI [auth 1]
BG [auth 7]
HF [auth 0]
JE [auth J]
KF [auth 8]
AI [auth 1],
BG [auth 7],
HF [auth 0],
JE [auth J],
KF [auth 8],
MH [auth 1],
PJ [auth 5],
SG [auth 3],
SI [auth 4],
TE [auth 0],
TG [auth 3],
WI [auth 6]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
BCR (Subject of Investigation/LOI)
Query on BCR

Download Ideal Coordinates CCD File 
CE [auth G]
DE [auth G]
DG [auth 7]
DI [auth 4]
EE [auth H]
CE [auth G],
DE [auth G],
DG [auth 7],
DI [auth 4],
EE [auth H],
FE [auth I],
HK [auth 5],
IE [auth J],
JF [auth 8],
KD [auth B],
LB [auth A],
LD [auth B],
LH [auth 1],
MB [auth A],
MD [auth B],
NB [auth A],
ND [auth B],
OB [auth A],
OD [auth B],
PB [auth A],
RB [auth A],
UD [auth F],
UG [auth 3],
VG [auth 3],
VI [auth 6],
XB [auth B],
XD [auth F]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT (Subject of Investigation/LOI)
Query on LMT

Download Ideal Coordinates CCD File 
JH [auth 3],
QD [auth B]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN (Subject of Investigation/LOI)
Query on PQN

Download Ideal Coordinates CCD File 
JB [auth A],
JD [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
IB [auth A],
SD [auth C],
TD [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.359 
  • R-Value Work: 0.291 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 194.57α = 90
b = 98.12β = 94.56
c = 210.13γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Science and TechnologyJapanJPMJCR13M4
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan16H06560

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 1.1: 2023-07-12
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description