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Entry
Database: PDB / ID: 4pbu
TitleSerial Time-resolved crystallography of Photosystem II using a femtosecond X-ray laser The S1 state
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 15
  • Cytochrome c-550
  • Photosystem Q(B) protein 1
KeywordsPHOTOSYNTHESIS / Photosystem II / Time resolved / Free electron laser
Function / homology
Function and homology information


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 / chlorophyll binding / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor ...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 / chlorophyll binding / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / 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 / oxidation-reduction process / electron transfer activity / iron ion binding / heme binding / integral component of membrane / metal ion binding
Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II PsbU, oxygen evolving complex / 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 PsbU, oxygen evolving complex / 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 PsbX / Photosystem II reaction centre protein Ycf12 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Photosystem II PsbZ, reaction centre / 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 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
Photosystem II 12 kDa extrinsic protein / Photosystem II reaction center protein K / Photosystem II reaction center protein I / Photosystem II reaction center protein Ycf12 / Photosystem II reaction center protein H / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein T / Cytochrome b559 subunit alpha / Photosystem II reaction center protein L / Cytochrome b559 subunit beta ...Photosystem II 12 kDa extrinsic protein / Photosystem II reaction center protein K / Photosystem II reaction center protein I / Photosystem II reaction center protein Ycf12 / Photosystem II reaction center protein H / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein T / Cytochrome b559 subunit alpha / Photosystem II reaction center protein L / Cytochrome b559 subunit beta / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein Z / Photosystem II reaction center protein M / Photosystem II D2 protein / Photosystem II reaction center protein J / Photosystem II protein D1 1 / Photosystem II manganese-stabilizing polypeptide / Cytochrome c-550 / Photosystem II reaction center X protein
Specimen sourceThermosynechococcus elongatus (Cyanobacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 5 Å
AuthorsKupitz, C. / Basu, S. / Grotjohann, I. / Fromme, R. / Zatsepin, N. / Rendek, K.N. / Hunter, M. / Shoeman, R.L. / White, T.A. / Wang, D. / James, D. / Yang, J.H. / Cobb, D.E. / Reeder, B. / Sierra, R.G. / Liu, H. / Barty, A. / Aquila, A. / Deponte, D. / Kirian, R.A. / Bari, S. / Bergkamp, J.J. / Beyerlein, K. / Bogan, M.J. / Caleman, C. / Chao, T.-C. / Conrad, C.E. / Davis, K.M. / Fleckenstein, H. / Galli, L. / Hau-Riege, S.P. / Kassemeyer, S. / Laksmono, H. / Liang, M. / Lomb, L. / Marchesini, S. / Martin, A.V. / Messerschmidt, M. / Milathianaki, D. / Nass, K. / Ros, A. / Roy-Chowdhury, S. / Schmidt, K. / Seibert, M. / Steinbrener, J. / Stellato, F. / Yan, L. / Yoon, C. / Moore, T.A. / Moore, A.L. / Pushkar, Y. / Williams, G.J. / Boutet, S. / Doak, R.B. / Weierstall, U. / Frank, M. / Chapman, H.N. / Spence, J.C.H. / Fromme, P.
Funding supportUnited States , Germany , 14件
OrganizationGrant numberCountry
Department of Energy (United States)DE-SC0001016United States
National Institutes of Health/National Institute of General Medical Sciences1R01GM095583United States
National Science Foundation (United States)MCB-1021557United States
National Science Foundation (United States)MCB- 1120997United States
German Research FoundationEXC 306Germany
German Research Foundation?Center for Ultrafast Imaging?Germany
Max Planck SocietyAtomic, Molecular and Optical Sciences ProgramGermany
Department of Energy (United States)Chemical Sciences Geosciences and Biosciences DivisionUnited States
SLACLDRDUnited States
Department of Energy (United States)DE-AC52- 07NA27344United States
UCOP Lab Fee Program118036United States
LLNL LDRD12-ERD-031United States
Hamburg Initiative for Excellence in ResearchHamburg Ministry of Science and Research and Joachim Herz StiftungGermany
National Science Foundation (United States)BioFEL Science Technology Center (award 1231306)United States
CitationJournal: Nature / Year: 2014
Title: Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser.
Authors: Kupitz, C. / Basu, S. / Grotjohann, I. / Fromme, R. / Zatsepin, N.A. / Rendek, K.N. / Hunter, M.S. / Shoeman, R.L. / White, T.A. / Wang, D. / James, D. / Yang, J.H. / Cobb, D.E. / Reeder, B. / Sierra, R.G. / Liu, H. / Barty, A. / Aquila, A.L. / Deponte, D. / Kirian, R.A. / Bari, S. / Bergkamp, J.J. / Beyerlein, K.R. / Bogan, M.J. / Caleman, C. / Chao, T.C. / Conrad, C.E. / Davis, K.M. / Fleckenstein, H. / Galli, L. / Hau-Riege, S.P. / Kassemeyer, S. / Laksmono, H. / Liang, M. / Lomb, L. / Marchesini, S. / Martin, A.V. / Messerschmidt, M. / Milathianaki, D. / Nass, K. / Ros, A. / Roy-Chowdhury, S. / Schmidt, K. / Seibert, M. / Steinbrener, J. / Stellato, F. / Yan, L. / Yoon, C. / Moore, T.A. / Moore, A.L. / Pushkar, Y. / Williams, G.J. / Boutet, S. / Doak, R.B. / Weierstall, U. / Frank, M. / Chapman, H.N. / Spence, J.C. / Fromme, P.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 13, 2014 / Release: Jul 16, 2014
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 16, 2014Structure modelrepositoryInitial release
1.1Jul 30, 2014Structure modelDatabase references
1.2Aug 6, 2014Structure modelStructure summary
1.3Oct 1, 2014Structure modelDatabase references
1.4Sep 23, 2015Structure modelData collection
1.5Sep 6, 2017Structure modelAuthor supporting evidence / Derived calculationspdbx_audit_support / pdbx_struct_oper_list_pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
1.6Nov 22, 2017Structure modelRefinement descriptionsoftware
1.7Sep 19, 2018Structure modelData collectiondiffrn_detector_diffrn_detector.detector

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Photosystem Q(B) protein 1
B: Photosystem II core light harvesting protein
C: Photosystem II CP43 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
a: Photosystem Q(B) protein 1
b: Photosystem II core light harvesting protein
c: Photosystem II CP43 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)692,590190
Polymers584,77338
Non-polymers107,818152
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)133.250, 226.260, 307.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain a
12chain B
22chain b
13chain C
23chain c
14chain D
24chain d
15chain E
25chain e
16chain F
26chain f
17chain H
27chain h
18chain I
28chain i
19chain J
29chain j
110chain K
210chain k
111chain L
211chain l
112chain M
212chain m
113chain O
213chain o
114chain T
214chain t
115chain U
215chain u
116chain V
216chain v
117chain X
217chain x
118chain Y
218chain y
119chain Z
219chain z

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
11chain AA11 - 667
21chain aa11 - 659
12chain BB2 - 668
22chain bb2 - 649
13chain CC23 - 661
23chain cc19 - 661
14chain DD11 - 714
24chain dd12 - 714
15chain EE4 - 772
25chain ee4 - 772
16chain FF12 - 641
26chain ff14 - 641
17chain HH2 - 663
27chain hh2 - 663
18chain II1 - 38
28chain ii1 - 38
19chain JJ3 - 40
29chain jj1 - 652
110chain KK10 - 653
210chain kk10 - 653
111chain LL1 - 668
211chain ll1 - 694
112chain MM1 - 34
212chain mm1 - 34
113chain OO4 - 767
213chain oo4 - 767
114chain TT1 - 647
214chain tt1 - 647
115chain UU8 - 808
215chain uu8 - 104
116chain VV1 - 642
216chain vv1 - 642
117chain XX2 - 40
217chain xx2 - 40
118chain YY18 - 46
218chain yy18 - 46
119chain ZZ1 - 62
219chain zz1 - 62

NCS ensembles:
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19

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Components

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Protein/peptide , 2 types, 4 molecules AaVv

#1: Protein/peptide Photosystem Q(B) protein 1 / 32 kDa thylakoid membrane protein 1 / Photosystem II protein D-1 / Photosystem II D-1 protein


Mass: 37029.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: P0A444, photosystem II
#16: Protein/peptide Cytochrome c-550 / Cytochrome c-549 / Cytochrome c550 / Low-potential cytochrome c


Mass: 15148.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: P0A386

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Photosystem II ... , 15 types, 30 molecules BbCcDdHhIiJjKkLlMmOoTtUuYyXxZz

#2: Protein/peptide Photosystem II core light harvesting protein / / Photosystem II CP47 protein


Mass: 55939.562 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: Q8DIQ1
#3: Protein/peptide Photosystem II CP43 protein /


Mass: 49668.758 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: Q8DIF8
#4: Protein/peptide Photosystem II D2 protein / / PSII D2 protein / Photosystem Q(A) protein / Photosystem II D2 protein


Mass: 38404.949 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
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 method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: Q8DJ43
#8: Protein/peptide Photosystem II reaction center protein I / / PSII-I / PSII 4.4 kDa protein


Mass: 4410.245 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: Q8DJZ6
#9: Protein/peptide Photosystem II reaction center protein J / / PSII-J


Mass: 4105.908 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
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 method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: Q9F1K9
#11: Protein/peptide Photosystem II reaction center protein L / / PSII-L / PSII 5 kDa protein


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


Mass: 3807.517 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: Q8DHA7
#13: Protein/peptide Photosystem II manganese-stabilizing polypeptide / / MSP


Mass: 26523.578 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: P0A431
#14: Protein/peptide Photosystem II reaction center protein T / / PSII-Tc


Mass: 3620.369 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
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 method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: Q9F1L5
#17: Protein/peptide Photosystem II reaction center protein Ycf12 /


Mass: 3098.921 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: Q8DJI1
#18: Protein/peptide Photosystem II reaction center X protein /


Mass: 4077.873 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
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 method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: Q8DHJ2

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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: 9321.515 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
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 method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: Q8DIN9

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Non-polymers , 14 types, 152 molecules

#20: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O5
#21: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Iron
#22: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl / Chloride
#23: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Bicarbonate
#24: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 70 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Chlorophyll a
#25: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5
#26: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C40H56 / Beta-Carotene
#27: 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 / Source method: obtained synthetically / Formula: C53H80O2
#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 / Source method: obtained synthetically / Formula: C41H78O12S
#29: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C38H75O10P
#30: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca / Calcium
#31: Chemical
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Mass: 949.299 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C51H96O15
#32: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Heme
#33: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Magnesium

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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: 3.96 Å3/Da / Density % sol: 68.92 %
Crystal growTemperature: 283 K / Method: liquid diffusion / pH: 7
Details: 100 mM Pipes pH 7.0, 5 mM CaCl2, 10 mM tocopherol, and 10-17% PEG 2000

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 2.04 Å
DetectorType: CS-PAD CXI-2 / Detector: PIXEL / Date: Jan 25, 2012 / Details: several days
RadiationMonochromator: None / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.04 Å / Relative weight: 1
ReflectionResolution: 5→100.638 Å / Num. all: 41704 / Num. obs: 40964 / % possible obs: 100 % / Redundancy: 684 % / Biso Wilson estimate: 285.07 Å2 / Net I/σ(I): 5.4
Reflection shellResolution: 5→5.123 Å / Redundancy: 617 % / Mean I/σ(I) obs: 2.1 / % possible all: 99

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Cheetahdata collection
CrystFELdata reduction
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ARC
Resolution: 5→100.638 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.262 2056 5.02 %
Rwork0.2606 38890 -
Obs0.2607 40946 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.03 Å2 / Biso mean: 33.7489 Å2 / Biso min: 13.83 Å2
Refinement stepCycle: final / Resolution: 5→100.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41296 0 7625 0 48921
Biso mean--37.34 --
Num. residues----5270
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.03951301
f_angle_d3.02970757
f_chiral_restr0.4917125
f_plane_restr0.028628
f_dihedral_angle_d21.65918204
Refine LS restraints NCS

Refinement-ID: X-RAY DIFFRACTION / Rms: 7.008 / Type: TORSIONAL

Ens-IDDom-IDAuth asym-IDNumber
11A3021
12a3021
21B4445
22b4445
31C4054
32c4054
41D3154
42d3154
51E735
52e735
61F290
62f290
71H568
72h568
81I342
82i342
91J312
92j312
101K336
102k336
111L348
112l348
121M302
122m302
131O2194
132o2194
141T273
142t273
151U930
152u930
161V1264
162v1264
171X313
172x313
181Y251
182y251
191Z531
192z531
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
5-5.11630.34341400.350225702710
5.1163-5.24420.36321340.324625322666
5.2442-5.3860.29851330.31225642697
5.386-5.54450.28341380.30825592697
5.5445-5.72350.28061280.295925312659
5.7235-5.9280.25171350.285925672702
5.928-6.16530.27311440.276625692713
6.1653-6.44590.25091360.260125792715
6.4459-6.78560.25031600.245425332693
6.7856-7.21070.24251160.240726172733
7.2107-7.76720.22211180.23626342752
7.7672-8.54850.20551350.207125882723
8.5485-9.78460.17191520.191626172769
9.7846-12.3240.21831460.202126492795
12.324-100.65830.34921410.330827812922

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