Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 
    0.331 (Depositor), 0.340 (DCC) 
  • R-Value Work: 
    0.324 (Depositor), 0.344 (DCC) 
  • R-Value Observed: 
    0.325 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

Macromolecular diffractive imaging using imperfect crystals.

Ayyer, K.Yefanov, O.M.Oberthur, D.Roy-Chowdhury, S.Galli, L.Mariani, V.Basu, S.Coe, J.Conrad, C.E.Fromme, R.Schaffer, A.Dorner, K.James, D.Kupitz, C.Metz, M.Nelson, G.Xavier, P.L.Beyerlein, K.R.Schmidt, M.Sarrou, I.Spence, J.C.Weierstall, U.White, T.A.Yang, J.H.Zhao, Y.Liang, M.Aquila, A.Hunter, M.S.Robinson, J.S.Koglin, J.E.Boutet, S.Fromme, P.Barty, A.Chapman, H.N.

(2016) Nature 530: 202-206

  • DOI: https://doi.org/10.1038/nature16949
  • Primary Citation Related Structures: 
    5E79, 5E7C

  • PubMed Abstract: 

    The three-dimensional structures of macromolecules and their complexes are mainly elucidated by X-ray protein crystallography. A major limitation of this method is access to high-quality crystals, which is necessary to ensure X-ray diffraction extends to sufficiently large scattering angles and hence yields information of sufficiently high resolution with which to solve the crystal structure. The observation that crystals with reduced unit-cell volumes and tighter macromolecular packing often produce higher-resolution Bragg peaks suggests that crystallographic resolution for some macromolecules may be limited not by their heterogeneity, but by a deviation of strict positional ordering of the crystalline lattice. Such displacements of molecules from the ideal lattice give rise to a continuous diffraction pattern that is equal to the incoherent sum of diffraction from rigid individual molecular complexes aligned along several discrete crystallographic orientations and that, consequently, contains more information than Bragg peaks alone. Although such continuous diffraction patterns have long been observed--and are of interest as a source of information about the dynamics of proteins--they have not been used for structure determination. Here we show for crystals of the integral membrane protein complex photosystem II that lattice disorder increases the information content and the resolution of the diffraction pattern well beyond the 4.5-ångström limit of measurable Bragg peaks, which allows us to phase the pattern directly. Using the molecular envelope conventionally determined at 4.5 ångströms as a constraint, we obtain a static image of the photosystem II dimer at a resolution of 3.5 ångströms. This result shows that continuous diffraction can be used to overcome what have long been supposed to be the resolution limits of macromolecular crystallography, using a method that exploits commonly encountered imperfect crystals and enables model-free phasing.


  • Organizational Affiliation
    • Center for Free-Electron Laser Science, DESY, 22607 Hamburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 702.16 kDa 
  • Atom Count: 50,074 
  • Modeled Residue Count: 5,264 
  • Deposited Residue Count: 5,264 
  • Unique protein chains: 19

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein D1 1A,
T [auth a]
334Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
U [auth b]
504Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
V [auth c]
451Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
W [auth d]
342Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
X [auth e]
81Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Y [auth f]
34Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HG [auth H],
Z [auth h]
65Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IAA [auth i],
H [auth I]
38Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JBA [auth j],
I [auth J]
38Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P59087 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KCA [auth k],
J [auth K]
37Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LDA [auth l],
K [auth L]
37Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MEA [auth m],
L [auth M]
34Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideFA [auth o],
M [auth O]
243Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TGA [auth t],
N [auth T]
30Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinHA [auth u],
O [auth U]
97Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c-550IA [auth v],
P [auth V]
137Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A386 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12JA [auth y],
Q [auth Y]
29Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinKA [auth x],
R [auth X]
39Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZLA [auth z],
S [auth Z]
62Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DHJ2 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence

Small Molecules

Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD



Download:Ideal Coordinates CCD File
CG [auth d]
ED [auth H]
KG [auth h]
LC [auth C]
MC [auth C]
CG [auth d],
ED [auth H],
KG [auth h],
LC [auth C],
MC [auth C],
NC [auth C],
SF [auth c],
TF [auth c],
UF [auth c],
YC [auth E]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA

Query on CLA



Download:Ideal Coordinates CCD File
AC [auth C]
AG [auth d]
BC [auth C]
CB [auth B]
CC [auth C]
AC [auth C],
AG [auth d],
BC [auth C],
CB [auth B],
CC [auth C],
DB [auth B],
DC [auth C],
DF [auth c],
EB [auth B],
EC [auth C],
EF [auth c],
FB [auth B],
FC [auth C],
FE [auth a],
FF [auth c],
GB [auth B],
GC [auth C],
GF [auth c],
HB [auth B],
HC [auth C],
HF [auth c],
IB [auth B],
IC [auth C],
IF [auth c],
JB [auth B],
JC [auth C],
JE [auth b],
JF [auth c],
KB [auth B],
KE [auth b],
KF [auth c],
LB [auth B],
LE [auth b],
LF [auth c],
MB [auth B],
ME [auth b],
MF [auth c],
NB [auth B],
NE [auth b],
NF [auth c],
OB [auth B],
OE [auth b],
OF [auth c],
PB [auth B],
PE [auth b],
PF [auth c],
QB [auth B],
QE [auth b],
RA [auth A],
RB [auth B],
RC [auth D],
RE [auth b],
SA [auth A],
SC [auth D],
SE [auth b],
TC [auth D],
TE [auth b],
UA [auth A],
UE [auth b],
VE [auth b],
WD [auth a],
WE [auth b],
XB [auth C],
XD [auth a],
XE [auth b],
YB [auth C],
YE [auth b],
ZB [auth C],
ZD [auth a],
ZF [auth d]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO

Query on PHO



Download:Ideal Coordinates CCD File
QC [auth D],
TA [auth A],
YD [auth a],
YF [auth d]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD

Query on SQD



Download:Ideal Coordinates CCD File
CE [auth a]
EE [auth a]
HE [auth b]
KD [auth L]
OG [auth l]
CE [auth a],
EE [auth a],
HE [auth b],
KD [auth L],
OG [auth l],
PD [auth X],
UG [auth x],
WB [auth B],
XA [auth A],
ZA [auth A]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG

Query on LMG



Download:Ideal Coordinates CCD File
CF [auth b]
DE [auth a]
LG [auth j]
OC [auth C]
PC [auth C]
CF [auth b],
DE [auth a],
LG [auth j],
OC [auth C],
PC [auth C],
QD [auth Z],
VB [auth B],
VF [auth c],
VG [auth z],
WF [auth c],
XC [auth D],
YA [auth A]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9

Query on PL9



Download:Ideal Coordinates CCD File
BE [auth a],
BG [auth d],
UC [auth D],
WA [auth A]
2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
LHG

Query on LHG



Download:Ideal Coordinates CCD File
AB [auth A]
DG [auth d]
EG [auth d]
FG [auth e]
GE [auth a]
AB [auth A],
DG [auth d],
EG [auth d],
FG [auth e],
GE [auth a],
JD [auth L],
PG [auth l],
VC [auth D],
WC [auth D],
ZC [auth E]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM

Query on HEM



Download:Ideal Coordinates CCD File
AD [auth E],
GG [auth e],
OD [auth V],
TG [auth v]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR

Query on BCR



Download:Ideal Coordinates CCD File
AE [auth a]
AF [auth b]
BD [auth F]
BF [auth b]
DD [auth H]
AE [auth a],
AF [auth b],
BD [auth F],
BF [auth b],
DD [auth H],
FD [auth I],
HD [auth K],
HG [auth f],
ID [auth K],
JG [auth h],
KC [auth C],
MD [auth T],
NG [auth k],
QF [auth c],
RF [auth c],
RG [auth t],
SB [auth B],
TB [auth B],
UB [auth B],
VA [auth A],
XF [auth c],
ZE [auth b]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
OEX

Query on OEX



Download:Ideal Coordinates CCD File
MA [auth A],
RD [auth a]
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT

Query on BCT



Download:Ideal Coordinates CCD File
QA [auth A],
VD [auth a]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2

Query on FE2



Download:Ideal Coordinates CCD File
NA [auth A],
SD [auth a]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
BB [auth B]
CD [auth F]
IE [auth b]
IG [auth f]
LD [auth O]
BB [auth B],
CD [auth F],
IE [auth b],
IG [auth f],
LD [auth O],
QG [auth o]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
ND [auth U]
OA [auth A]
PA [auth A]
SG [auth u]
TD [auth a]
ND [auth U],
OA [auth A],
PA [auth A],
SG [auth u],
TD [auth a],
UD [auth a]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
GD [auth J],
MG [auth j]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free:  0.331 (Depositor), 0.340 (DCC) 
  • R-Value Work:  0.324 (Depositor), 0.344 (DCC) 
  • R-Value Observed: 0.325 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 250.8α = 90
b = 250.8β = 90
c = 250.8γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Advisory, Data collection
  • Version 1.2: 2018-08-08
    Changes: Data collection, Database references
  • Version 1.3: 2018-11-14
    Changes: Data collection
  • Version 2.0: 2023-12-13
    Changes: Advisory, Data collection, Database references, Derived calculations, Non-polymer description
  • Version 2.1: 2024-01-10
    Changes: Refinement description
  • Version 2.2: 2024-10-16
    Changes: Structure summary