5E79

Macromolecular diffractive imaging using imperfect crystals


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.324 
  • R-Value Observed: 0.325 

wwPDB Validation   3D Report Full Report


This is version 2.1 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 of 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

    School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA.


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
Find proteins for P0A444 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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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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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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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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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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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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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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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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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
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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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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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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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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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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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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
Find proteins for Q9F1L5 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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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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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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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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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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Small Molecules
Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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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

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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

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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

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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

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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

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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

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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

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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

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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

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MA [auth A],
RD [auth a]
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT
Query on BCT

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QA [auth A],
VD [auth a]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2

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NA [auth A],
SD [auth a]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA
Query on CA

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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

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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

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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 
  • R-Value Work: 0.324 
  • R-Value Observed: 0.325 
  • Space Group: P 1
  • Diffraction Data: https://doi.org/10.11577/1341415
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

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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