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- PDB-6dhe: RT XFEL structure of the dark-stable state of Photosystem II (0F,... -

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Entry
Database: PDB / ID: 6dhe
TitleRT XFEL structure of the dark-stable state of Photosystem II (0F, S1-rich) at 2.05 Angstrom resolution
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 17
  • Cytochrome c-550
KeywordsPHOTOSYNTHESIS / PHOTOSYSTEMS / TRANSMEMBRANE / ROOM TEMPERATURE / ELECTRON TRANSPORT
Function / homologyPhotosystem II PsbV, cytochrome c-550 precursor / Photosystem II reaction centre protein Ycf12 / Photosystem II PsbL / Photosystem II PsbI / Photosystem II PsbK / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II CP43 reaction centre protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit ...Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II reaction centre protein Ycf12 / Photosystem II PsbL / Photosystem II PsbI / Photosystem II PsbK / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II CP43 reaction centre protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II PsbM / Cytochrome c-like domain / Photosystem II PsbY / Photosystem II PsbX / Photosystem II PsbU, oxygen evolving complex / Photosystem II PsbZ, reaction centre / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II cytochrome c-550 precursor / Photosystem II CP47 reaction centre protein / Photosystem II PsbT superfamily / Photosystem II PsbX, type 1 subfamily / Cytochrome c-550 domain / Photosystem antenna protein-like superfamily / Photosystem II PsbZ superfamily / Photosystem II protein D1/D2 superfamily / Photosystem II reaction centre protein H superfamily / Cytochrome c-like domain superfamily / Photosystem II cytochrome b559, alpha subunit superfamily / Photosystem II PsbJ / Photosystem II PsbO, manganese-stabilising / Photosystem II PsbJ superfamily / Photosystem II PsbT / Cytochrome c family profile. / Cytochrome b559 subunits heme-binding site signature. / Photosynthetic reaction center proteins signature. / Cytochrome c-550 domain / Photosystem II reaction centre X protein (PsbX) / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II protein Y (PsbY) / Photosystem II complex subunit Ycf12 / Photosystem II reaction centre M protein (PsbM) / Photosystem II 4 kDa reaction centre component / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / PsbL protein / PsbJ / YCF9 / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II PsbI superfamily / Photosystem II reaction centre protein H / Photosystem antenna protein-like / Photosynthetic reaction centre, L/M / Photosystem II PsbM superfamily / Photosystem II PsbK superfamily / Photosynthetic reaction centre protein / Photosystem II reaction centre T protein / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Photosystem II protein / Photosystem II 10 kDa phosphoprotein / Photosystem II PsbL superfamily / oxygen evolving activity / photosystem II reaction center / photosystem II stabilization / photosystem II / photosystem II assembly / photosystem II oxygen evolving complex / photosystem II / cytochrome c-heme linkage / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / chlorophyll binding / thylakoid membrane / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / respiratory electron transport chain / phosphate ion binding / response to herbicide / photosynthesis / extrinsic component of membrane / protein-chromophore linkage / protein stabilization / manganese ion binding / oxidation-reduction process / electron transfer activity / iron ion binding / heme binding / integral component of membrane / metal ion binding / Cytochrome b559 subunit alpha / Photosystem II 12 kDa extrinsic protein / Photosystem II reaction center protein K / Photosystem II protein Y / Photosystem II reaction center protein I / Photosystem II reaction center protein Ycf12 / Photosystem II reaction center protein H / Photosystem II CP47 reaction center protein
Function and homology information
Specimen sourceThermosynechococcus elongatus (Cyanobacteria)
Thermosynechococcus elongatus BP-1 (Cyanobacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / 2.05 Å resolution
AuthorsKern, J. / Chatterjee, R. / Young, I.D. / Fuller, F.D. / Lassalle, L. / Ibrahim, M. / Gul, S. / Fransson, T. / Brewster, A.S. / Alonso-Mori, R. / Hussein, R. / Zhang, M. / Douthit, L. / de Lichtenberg, C. / Cheah, M.H. / Shevela, D. / Wersig, J. / Seufert, I. / Sokaras, D. / Pastor, E. / Weninger, C. / Kroll, T. / Sierra, R.G. / Aller, P. / Butryn, A. / Orville, A.M. / Liang, M. / Batyuk, A. / Koglin, J.E. / Carbajo, S. / Boutet, S. / Moriarty, N.W. / Holton, J.M. / Dobbek, H. / Adams, P.D. / Bergmann, U. / Sauter, N.K. / Zouni, A. / Messinger, J. / Yano, J. / Yachandra, V.K.
CitationJournal: Nature / Year: 2018
Title: Structures of the intermediates of Kok's photosynthetic water oxidation clock.
Authors: Kern, J. / Chatterjee, R. / Young, I.D. / Fuller, F.D. / Lassalle, L. / Ibrahim, M. / Gul, S. / Fransson, T. / Brewster, A.S. / Alonso-Mori, R. / Hussein, R. / Zhang, M. / Douthit, L. / de Lichtenberg, C. / Cheah, M.H. / Shevela, D. / Wersig, J. / Seuffert, I. / Sokaras, D. / Pastor, E. / Weninger, C. / Kroll, T. / Sierra, R.G. / Aller, P. / Butryn, A. / Orville, A.M. / Liang, M. / Batyuk, A. / Koglin, J.E. / Carbajo, S. / Boutet, S. / Moriarty, N.W. / Holton, J.M. / Dobbek, H. / Adams, P.D. / Bergmann, U. / Sauter, N.K. / Zouni, A. / Messinger, J. / Yano, J. / Yachandra, V.K.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 20, 2018 / Release: Nov 21, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 21, 2018Structure modelrepositoryInitial release
1.1Nov 28, 2018Structure modelData collection / Database referencescitation / diffrn_radiation_wavelength / diffrn_source_citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Photosystem II protein D1 1
B: Photosystem II CP47 reaction center protein
C: Photosystem II CP43 reaction center protein
D: Photosystem II D2 protein
E: Cytochrome b559 subunit alpha
F: Cytochrome b559 subunit beta
H: Photosystem II reaction center protein H
I: Photosystem II reaction center protein I
J: Photosystem II reaction center protein J
K: Photosystem II reaction center protein K
L: Photosystem II reaction center protein L
M: Photosystem II reaction center protein M
O: Photosystem II manganese-stabilizing polypeptide
T: Photosystem II reaction center protein T
U: Photosystem II 12 kDa extrinsic protein
V: Cytochrome c-550
Y: Photosystem II reaction center protein Ycf12
X: Photosystem II reaction center X protein
Z: Photosystem II reaction center protein Z
R: Photosystem II protein Y
a: Photosystem II protein D1 1
b: Photosystem II CP47 reaction center protein
c: Photosystem II CP43 reaction center protein
d: Photosystem II D2 protein
e: Cytochrome b559 subunit alpha
f: Cytochrome b559 subunit beta
h: Photosystem II reaction center protein H
i: Photosystem II reaction center protein I
j: Photosystem II reaction center protein J
k: Photosystem II reaction center protein K
l: Photosystem II reaction center protein L
m: Photosystem II reaction center protein M
o: Photosystem II manganese-stabilizing polypeptide
t: Photosystem II reaction center protein T
u: Photosystem II 12 kDa extrinsic protein
v: Cytochrome c-550
y: Photosystem II reaction center protein Ycf12
x: Photosystem II reaction center X protein
z: Photosystem II reaction center protein Z
r: Photosystem II protein Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)730,695226
Polyers590,60840
Non-polymers140,087186
Water36,4082021
1


  • idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)116.906, 221.407, 308.668
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP 21 21 21

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Components

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Photosystem II ... , 17 types, 34 molecules AaBbCcDdHhIiJjKkLlMmOoTtUuYyXx...

#1: Protein/peptide Photosystem II protein D1 1 / / PSII D1 protein 1 / Photosystem II Q(B) protein 1


Mass: 37059.258 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: P0A444, photosystem II
#2: Protein/peptide Photosystem II CP47 reaction center protein / / PSII 47 kDa protein / Protein CP-47


Mass: 56096.758 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q8DIQ1
#3: Protein/peptide Photosystem II CP43 reaction center protein / / PSII 43 kDa protein / Protein CP-43


Mass: 49207.250 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q8DIF8
#4: Protein/peptide Photosystem II D2 protein / / PSII D2 protein / Photosystem II Q(A) protein


Mass: 38275.836 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q8CM25, photosystem II
#7: Protein/peptide Photosystem II reaction center protein H / / PSII-H


Mass: 7227.559 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q8DJ43
#8: Protein/peptide Photosystem II reaction center protein I / / PSII-I / PSII 4.4 kDa protein


Mass: 4195.983 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q8DJZ6
#9: Protein/peptide Photosystem II reaction center protein J / / PSII-J


Mass: 3627.325 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: P59087
#10: Protein/peptide Photosystem II reaction center protein K / / PSII-K


Mass: 4101.911 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q9F1K9
#11: Protein/peptide Photosystem II reaction center protein L / / PSII-L


Mass: 4299.044 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q8DIN8
#12: Protein/peptide Photosystem II reaction center protein M / / PSII-M


Mass: 3706.348 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q8DHA7
#13: Protein/peptide Photosystem II manganese-stabilizing polypeptide / / MSP


Mass: 26651.707 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: P0A431
#14: Protein/peptide Photosystem II reaction center protein T / / PSII-Tc


Mass: 3648.379 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q8DIQ0
#15: Protein/peptide Photosystem II 12 kDa extrinsic protein / / PS II complex 12 kDa extrinsic protein / PSII-U


Mass: 10966.317 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q9F1L5
#17: Protein/peptide Photosystem II reaction center protein Ycf12 /


Mass: 3228.035 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q8DJI1
#18: Protein/peptide Photosystem II reaction center X protein /


Mass: 3990.795 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q9F1R6
#19: Protein/peptide Photosystem II reaction center protein Z / / PSII-Z


Mass: 6766.187 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q8DHJ2
#20: Protein/peptide Photosystem II protein Y /


Mass: 3859.732 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q8DKM3

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Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf

#5: Protein/peptide Cytochrome b559 subunit alpha / / PSII reaction center subunit V


Mass: 9378.566 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q8DIP0
#6: Protein/peptide Cytochrome b559 subunit beta / / PSII reaction center subunit VI


Mass: 3868.611 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: Q8DIN9

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Protein/peptide , 1 types, 2 molecules Vv

#16: Protein/peptide Cytochrome c-550 / Cytochrome c-549 / Cytochrome c550 / Low-potential cytochrome c


Mass: 15148.255 Da / Num. of mol.: 2
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Details: cell / Strain: BP-1 / References: UniProt: P0A386

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Non-polymers , 16 types, 2207 molecules

#21: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Formula: Fe
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
Details: cell / Strain: BP-1 / Iron
#22: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Formula: Cl / Chloride
#23: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 70 / Formula: C55H72MgN4O5 / Chlorophyll a
#24: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 4 / Formula: C55H74N4O5
#25: Chemical
ChemComp-8CT / (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene


Mass: 536.873 Da / Num. of mol.: 12 / Formula: C40H56
#26: Chemical
ChemComp-PL9 / 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 / PLASTOQUINONE 9


Mass: 749.201 Da / Num. of mol.: 4 / Formula: C53H80O2
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
Details: cell / Strain: BP-1
#27: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 13 / Formula: C45H86O10
#28: Chemical
ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 8 / Formula: C41H78O12S
#29: Chemical
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Mass: 949.299 Da / Num. of mol.: 10 / Formula: C51H96O15
#30: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 2 / Formula: CaMn4O5
#31: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 10 / Formula: C40H56 / Beta-Carotene
#32: Chemical...
ChemComp-UNL / UNKNOWN LIGAND


Mass: 722.970 Da / Num. of mol.: 31
#33: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / PSII-Z


Mass: 722.970 Da / Num. of mol.: 10 / Formula: C38H75O10P
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
Details: cell / Strain: BP-1
#34: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Formula: CHO3 / Bicarbonate
#35: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Formula: C34H32FeN4O4 / Heme
#36: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2021 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.4 / Density percent sol: 63.79 % / Description: Cube-like crystals
Crystal growTemp: 298 K / Method: batch mode / pH: 6.5 / Details: 0.1 M MES pH 6.5, 0.1 M NH4Cl, 35% (w/v) PEG 5000

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Data collection

Diffraction
IDMean temperatureCrystal IDSerial crystal experiment
12981Y
32981Y
22981Y
Source
SourceTypeSynchrotron siteBeamlineIdWavelength
FREE ELECTRON LASERSLAC LCLS BEAMLINE MFXSLAC LCLSMFX11.305
FREE ELECTRON LASERSLAC LCLS BEAMLINE MFXSLAC LCLSMFX31.305
FREE ELECTRON LASERSLAC LCLS BEAMLINE MFXSLAC LCLSMFX21.305
Detector
TypeIdDetailsDetectorCollection date
RAYONIX MX170-HS1Compound refractive lensesCCD2016-07-14
RAYONIX MX170-HS3Compound refractive lensesCCD2017-07-13
RAYONIX MX170-HS2Compound refractive lensesCCD2016-10-20
Radiation
IdMonochromatorDiffraction protocolMonochromatic or laue m lScattering typeWavelength ID
1noneSINGLE WAVELENGTHMx-ray1
3noneSINGLE WAVELENGTHMx-ray2
2noneSINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelengthRelative weight
11.3051.0
21.3051.0
31.3051.0
ReflectionB iso Wilson estimate: 33.09 / D resolution high: 2.05 / D resolution low: 30.55 / Number obs: 497372 / CC half: .987 / NetI over sigmaI: 16.581 / Redundancy: 245.79 % / Percent possible obs: 99.96
Reflection shell
Highest resolutionLowest resolutionMeanI over sigI obsCC halfDiffraction IDRedundancyPercent possible all
5.56530.55132.601.9931896.6099.24
4.4175.56569.615.983631.17100.00
3.8584.41744.812.977558.95100.00
3.5053.85824.325.964515.91100.00
3.2543.50515.382.943483.70100.00
3.0623.2548.928.897437.34100.00
2.9093.0625.742.829345.17100.00
2.7822.9094.228.739217.86100.00
2.6752.7823.363.628156.80100.00
2.5832.6752.682.515120.79100.00
2.5022.5832.344.41397.98100.00
2.4312.5022.046.30381.32100.00
2.3672.4311.798.21068.58100.00
2.3092.3671.643.15159.20100.00
2.2562.3091.463.09751.40100.00
2.2082.2561.307.07944.09100.00
2.1642.2081.176.05737.23100.00
2.1232.1640.946.01128.82100.00
2.0852.1230.740.01720.36100.00
2.0502.0850.530.01812.5899.95

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Processing

Software
NameVersionClassification
PHENIXdev_svnrefinement
PDB_EXTRACT3.24data extraction
cctbx.xfeldata reduction
PHASERdev_svnphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KAF

5kaf


Overall SU ML: 0.33 / Cross valid method: THROUGHOUT / Sigma F: 1.33 / Overall phase error: 27.54
Solvent computationSolvent shrinkage radii: 0.9 / Solvent vdw probe radii: 1.11
Displacement parametersB iso max: 170.66 / B iso mean: 45.0801 / B iso min: 13.3
Least-squares processR factor R free: 0.2413 / R factor R work: 0.1846 / R factor obs: 0.1851 / Highest resolution: 2.05 / Lowest resolution: 30.552 / Number reflection R free: 4403 / Number reflection obs: 496416 / Percent reflection R free: 0.89 / Percent reflection obs: 99.8
Refine hist #finalHighest resolution: 2.05 / Lowest resolution: 30.552 / B iso mean ligand: 48.58 / B iso mean solvent: 42.41 / Number residues total: 5306
Number of atoms included #finalProtein: 41576 / Nucleic acid: 0 / Ligand: 19177 / Solvent: 1882 / Total: 62635
Refine LS shell

Refine ID: X-RAY DIFFRACTION / R factor R free error: 0 / Total number of bins used: 30

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
2.05000.35940.35552.0733134156961583097.0000
2.07330.38120.34642.0977147161641631199.0000
2.09770.35720.33522.12331431636516508100.0000
2.12330.38350.32872.15011501624816398100.0000
2.15010.36200.31842.17841491630616455100.0000
2.17840.35100.31312.20821401640716547100.0000
2.20820.35020.30232.23981501628016430100.0000
2.23980.35520.29012.27321441630516449100.0000
2.27320.31750.28372.30871451633516480100.0000
2.30870.34560.27172.34651481635316501100.0000
2.34650.30970.26142.38701451639816543100.0000
2.38700.29670.25272.43041501634016490100.0000
2.43040.30790.24012.47711451634616491100.0000
2.47710.26950.22882.52761501631316463100.0000
2.52760.32600.22272.58261451643016575100.0000
2.58260.25400.21092.64261451635216497100.0000
2.64260.23000.20012.70871471639316540100.0000
2.70870.28680.19552.78191461640016546100.0000
2.78190.26320.19822.86371471635716504100.0000
2.86370.27840.19432.95601501642616576100.0000
2.95600.24730.19093.06161461642016566100.0000
3.06160.24010.17793.18401481644016588100.0000
3.18400.24460.16593.32881461647316619100.0000
3.32880.22900.15783.50401481645416602100.0000
3.50400.20220.14543.72321501652016670100.0000
3.72320.18940.13694.01011471651416661100.0000
4.01010.17930.12644.41261481654916697100.0000
4.41260.16420.12315.04861481658616734100.0000
5.04860.21670.14506.35131501671916869100.0000
6.35130.20130.142830.5559152171241727699.0000

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New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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