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- PDB-7cjj: Photosystem II structure in the S2 state -

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Basic information

Entry
Database: PDB / ID: 7cjj
TitlePhotosystem II structure in the S2 state
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 17
  • Cytochrome c-550
KeywordsPHOTOSYNTHESIS / Photosystem II
Function / homology
Function and homology information


photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem II / response to herbicide ...photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem II / response to herbicide / extrinsic component of membrane / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthetic electron transport in photosystem II / : / phosphate ion binding / photosynthesis, light reaction / photosynthesis / respiratory electron transport chain / manganese ion binding / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II cytochrome b559, alpha subunit / Photosystem II protein Y (PsbY) / Photosystem II PsbY / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosynthetic Reaction Center, subunit M; domain 1 ...Photosystem II cytochrome b559, alpha subunit / Photosystem II protein Y (PsbY) / Photosystem II PsbY / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II PsbI / Photosystem II CP47 reaction centre protein / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II reaction centre protein H superfamily / Photosystem II 10 kDa phosphoprotein / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Cytochrome b559 subunits heme-binding site signature. / : / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Unknown ligand / Photosystem II CP47 reaction center protein / Photosystem II extrinsic protein O / Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein X / Photosystem II reaction center protein Z / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Photosystem II extrinsic protein V / Photosystem II reaction center protein Y / Cytochrome b559 subunit alpha / Cytochrome b559 subunit beta / Photosystem II reaction center protein I / Photosystem II reaction center protein L / Photosystem II reaction center protein M / Photosystem II reaction center protein T / Photosystem II reaction center protein H / Photosystem II reaction center protein K / Photosystem II protein D1 / Photosystem II extrinsic protein U / Photosystem II reaction center protein J
Similarity search - Component
Biological speciesThermosynechococcus vulcanus (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLi, H. / Shen, J.-R. / Suga, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Iucrj / Year: 2021
Title: Capturing structural changes of the S 1 to S 2 transition of photosystem II using time-resolved serial femtosecond crystallography.
Authors: Li, H. / Nakajima, Y. / Nomura, T. / Sugahara, M. / Yonekura, S. / Chan, S.K. / Nakane, T. / Yamane, T. / Umena, Y. / Suzuki, M. / Masuda, T. / Motomura, T. / Naitow, H. / Matsuura, Y. / ...Authors: Li, H. / Nakajima, Y. / Nomura, T. / Sugahara, M. / Yonekura, S. / Chan, S.K. / Nakane, T. / Yamane, T. / Umena, Y. / Suzuki, M. / Masuda, T. / Motomura, T. / Naitow, H. / Matsuura, Y. / Kimura, T. / Tono, K. / Owada, S. / Joti, Y. / Tanaka, R. / Nango, E. / Akita, F. / Kubo, M. / Iwata, S. / Shen, J.R. / Suga, M.
History
DepositionJul 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.0Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_validate_chiral
Item: _chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Photosystem II protein D1
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
X: Photosystem II reaction center protein X
Y: Photosystem II reaction center protein Ycf12
Z: Photosystem II reaction center protein Z
R: Photosystem II protein Y
a: Photosystem II protein D1
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
x: Photosystem II reaction center protein X
y: Photosystem II reaction center protein Ycf12
z: Photosystem II reaction center protein Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)723,664255
Polymers596,84939
Non-polymers126,815216
Water36,9492051
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.750, 231.630, 288.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Photosystem II ... , 17 types, 33 molecules AaBbCcDdHhIiJjKkLlMmOoTtUuXxYy...

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


Mass: 38235.602 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P51765, photosystem II
#2: Protein Photosystem II CP47 reaction center protein / PSII 47 kDa protein / Protein CP-47


Mass: 56068.742 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR1
#3: Protein Photosystem II CP43 reaction center protein / PSII 43 kDa protein / Protein CP-43


Mass: 49668.758 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR7
#4: Protein Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein


Mass: 38404.949 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR8, photosystem II
#7: Protein 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 vulcanus (bacteria) / References: UniProt: P19052
#8: Protein/peptide Photosystem II reaction center protein I / PSII-I / PSII 4.4 kDa protein


Mass: 4438.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12240
#9: Protein/peptide Photosystem II reaction center protein J / PSII-J


Mass: 3974.712 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: Q7DGD4
#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 vulcanus (bacteria) / References: UniProt: P19054
#11: Protein/peptide Photosystem II reaction center protein L / PSII-L


Mass: 4299.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12241
#12: Protein/peptide Photosystem II reaction center protein M / PSII-M


Mass: 4009.682 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12312
#13: Protein Photosystem II manganese-stabilizing polypeptide / MSP


Mass: 26651.707 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR2
#14: Protein/peptide Photosystem II reaction center protein T / PSII-Tc


Mass: 3906.738 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12313
#15: Protein Photosystem II 12 kDa extrinsic protein / PS II complex 12 kDa extrinsic protein / PSII-U


Mass: 11655.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P56152
#17: Protein/peptide Photosystem II reaction center protein X


Mass: 4191.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR4
#18: Protein/peptide Photosystem II reaction center protein Ycf12


Mass: 3228.035 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR3
#19: Protein 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 vulcanus (bacteria) / References: UniProt: D0VWR5
#20: Protein/peptide Photosystem II protein Y


Mass: 3859.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P0DM37

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

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


Mass: 9580.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12238
#6: Protein/peptide Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 4936.704 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12239

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Protein , 1 types, 2 molecules Vv

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


Mass: 15148.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P0A387

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Sugars , 3 types, 33 molecules

#32: Sugar
ChemComp-HTG / heptyl 1-thio-beta-D-glucopyranoside / HEPTYL 1-THIOHEXOPYRANOSIDE / heptyl 1-thio-beta-D-glucoside / heptyl 1-thio-D-glucoside / heptyl 1-thio-glucoside


Type: D-saccharide / Mass: 294.408 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C13H26O5S / Comment: detergent*YM
#33: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#35: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 18 types, 2234 molecules

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


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


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


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


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


Mass: 536.873 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C40H56
#26: 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
#27: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#28: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O5
#29: 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: isolated from a natural source / Formula: C53H80O2
#30: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 18 / Source method: obtained synthetically
#31: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#34: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C45H86O10
#36: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#37: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3
#38: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#39: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#40: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#41: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2051 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY
Nonpolymer detailsLigands assigned with UNL cannot be identified and were built as lipids or detergents.
Sequence detailsABOUT PRO A(a) 279, LEU K(k) 33, TRP K(k) 39 AND LEU M(m) 8, THE AUTHOR CONFIRMED BY ELECTRON ...ABOUT PRO A(a) 279, LEU K(k) 33, TRP K(k) 39 AND LEU M(m) 8, THE AUTHOR CONFIRMED BY ELECTRON DENSITY MAP. SEQUENCE DIFFERENCES OF CHAIN C(c) ARE BASED ON THE DATABASE SEQUENCE FROM THERMOSYNECHOCOCCUS ELONGATUS Q8DIF8_THEEB.

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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: 3.58 Å3/Da / Density % sol: 65.64 %
Crystal growTemperature: 293 K / Method: batch mode / Details: PEG, magnesium sulfate

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.77 Å
DetectorType: MPCCD / Detector: CCD / Date: Apr 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 329844 / % possible obs: 100 % / Redundancy: 235 % / Biso Wilson estimate: 50.81 Å2 / CC1/2: 0.997 / Net I/σ(I): 37
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 32695 / CC1/2: 0.54

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: dark structure

Resolution: 2.4→39.902 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2184 15900 5.03 %
Rwork0.1677 300173 -
obs0.1703 316073 96.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 205.78 Å2 / Biso mean: 63.1053 Å2 / Biso min: 30.28 Å2
Refinement stepCycle: final / Resolution: 2.4→39.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41493 0 9403 2080 52976
Biso mean--71.18 66.2 -
Num. residues----5289
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.42730.34145410.306310264100
2.4273-2.45580.34445420.296710259100
2.4558-2.48580.33035170.28610300100
2.4858-2.51720.31755570.257510289100
2.5172-2.55030.29475020.241410232100
2.5503-2.58530.32685440.24410282100
2.5853-2.62220.30375860.23810251100
2.6222-2.66130.28565270.224410235100
2.6613-2.70290.26935510.210510194100
2.7029-2.74720.26145570.200810271100
2.7472-2.79460.26435490.199110251100
2.7946-2.84540.25995320.19081016299
2.8454-2.90010.26675190.18121022299
2.9001-2.95930.26785530.18731011898
2.9593-3.02360.26155090.18151009998
3.0236-3.09390.25255170.18241005297
3.0939-3.17120.2545420.1795994296
3.1712-3.25690.23665180.1727984895
3.2569-3.35270.22635510.1717971294
3.3527-3.46090.23454980.164960393
3.4609-3.58450.22525190.1614947692
3.5845-3.72790.21494780.1562945191
3.7279-3.89750.22065090.1571939491
3.8975-4.10280.20595090.1491940991
4.1028-4.35950.19114660.1364952591
4.3595-4.69560.15995670.1281970294
4.6956-5.16730.17434850.1325995695
5.1673-5.91290.19935240.1477988894
5.9129-7.44170.18675340.1451013996
7.4417-39.9020.18075970.16641064798
Refinement TLS params.Method: refined / Origin x: 13.6749 Å / Origin y: -14.4457 Å / Origin z: -25.4671 Å
111213212223313233
T0.5571 Å2-0.0398 Å2-0.0399 Å2-0.3186 Å20.0413 Å2--0.2767 Å2
L0.2027 °2-0.0804 °2-0.0275 °2-0.4192 °20.1093 °2--0.4649 °2
S-0.0101 Å °-0.0315 Å °-0.0054 Å °0.0363 Å °0.0294 Å °-0.0214 Å °-0.0363 Å °-0 Å °-0.0199 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA11 - 344
2X-RAY DIFFRACTION1allA401 - 630
3X-RAY DIFFRACTION1allB2 - 505
4X-RAY DIFFRACTION1allB601 - 901
5X-RAY DIFFRACTION1allC23 - 473
6X-RAY DIFFRACTION1allC501 - 744
7X-RAY DIFFRACTION1allD11 - 352
8X-RAY DIFFRACTION1allD404 - 622
9X-RAY DIFFRACTION1allE4 - 84
10X-RAY DIFFRACTION1allE101 - 215
11X-RAY DIFFRACTION1allF12 - 45
12X-RAY DIFFRACTION1allF101 - 204
13X-RAY DIFFRACTION1allH2 - 65
14X-RAY DIFFRACTION1allH101 - 219
15X-RAY DIFFRACTION1allI1 - 38
16X-RAY DIFFRACTION1allI101 - 206
17X-RAY DIFFRACTION1allJ2 - 39
18X-RAY DIFFRACTION1allJ101 - 205
19X-RAY DIFFRACTION1allK10 - 46
20X-RAY DIFFRACTION1allK101 - 206
21X-RAY DIFFRACTION1allL2 - 37
22X-RAY DIFFRACTION1allL101 - 203
23X-RAY DIFFRACTION1allM1 - 33
24X-RAY DIFFRACTION1allM101 - 207
25X-RAY DIFFRACTION1allO4 - 246
26X-RAY DIFFRACTION1allO301 - 501
27X-RAY DIFFRACTION1allT1 - 30
28X-RAY DIFFRACTION1allT101 - 209
29X-RAY DIFFRACTION1allU9 - 104
30X-RAY DIFFRACTION1allU201 - 301
31X-RAY DIFFRACTION1allV1 - 137
32X-RAY DIFFRACTION1allV202 - 367
33X-RAY DIFFRACTION1allX2 - 39
34X-RAY DIFFRACTION1allX101 - 201
35X-RAY DIFFRACTION1allY18 - 46
36X-RAY DIFFRACTION1allY101 - 201
37X-RAY DIFFRACTION1allZ1 - 62
38X-RAY DIFFRACTION1allZ101
39X-RAY DIFFRACTION1allR2 - 35
40X-RAY DIFFRACTION1alla11 - 344
41X-RAY DIFFRACTION1alla401 - 633
42X-RAY DIFFRACTION1allb2 - 505
43X-RAY DIFFRACTION1allb601 - 901
44X-RAY DIFFRACTION1allc19 - 473
45X-RAY DIFFRACTION1allc501 - 742
46X-RAY DIFFRACTION1alld12 - 352
47X-RAY DIFFRACTION1alld402 - 614
48X-RAY DIFFRACTION1alle6 - 84
49X-RAY DIFFRACTION1alle101 - 208
50X-RAY DIFFRACTION1allf15 - 45
51X-RAY DIFFRACTION1allf102 - 204
52X-RAY DIFFRACTION1allh2 - 65
53X-RAY DIFFRACTION1allh101 - 216
54X-RAY DIFFRACTION1alli1 - 38
55X-RAY DIFFRACTION1alli101 - 203
56X-RAY DIFFRACTION1allj1 - 39
57X-RAY DIFFRACTION1allj101 - 202
58X-RAY DIFFRACTION1allk10 - 46
59X-RAY DIFFRACTION1allk101 - 203
60X-RAY DIFFRACTION1alll2 - 37
61X-RAY DIFFRACTION1alll101 - 204
62X-RAY DIFFRACTION1allm1 - 34
63X-RAY DIFFRACTION1allm101 - 215
64X-RAY DIFFRACTION1allo4 - 246
65X-RAY DIFFRACTION1allo301 - 501
66X-RAY DIFFRACTION1allt1 - 30
67X-RAY DIFFRACTION1allt101 - 206
68X-RAY DIFFRACTION1allu8 - 104
69X-RAY DIFFRACTION1allu201 - 247
70X-RAY DIFFRACTION1allv1 - 137
71X-RAY DIFFRACTION1allv201 - 346
72X-RAY DIFFRACTION1allx2 - 39
73X-RAY DIFFRACTION1allx101 - 202
74X-RAY DIFFRACTION1ally18 - 46
75X-RAY DIFFRACTION1ally101 - 201
76X-RAY DIFFRACTION1allz1 - 62
77X-RAY DIFFRACTION1allz101
78X-RAY DIFFRACTION1allG1 - 461

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