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- PDB-8gn2: Crystal structure of PPBQ-bound photosystem II complex -

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Basic information

Entry
Database: PDB / ID: 8gn2
TitleCrystal structure of PPBQ-bound photosystem II complex
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 17
  • Cytochrome c-550
KeywordsPHOTOSYNTHESIS / Photosystem / electron transfer / electron acceptor / Quinone
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 12 kDa extrinsic protein / Photosystem II PsbZ, reaction centre / Photosystem II CP47 reaction center protein / Photosystem II CP47 reaction center protein / 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 12 kDa extrinsic protein / Photosystem II PsbZ, reaction centre / Photosystem II CP47 reaction center protein / Photosystem II CP47 reaction center protein / 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 / DNA polymerase; domain 1 / Helix Hairpins / Roll / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 2-phenylcyclohexa-2,5-diene-1,4-dione / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 2-phenylcyclohexa-2,5-diene-1,4-dione / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / (3R)-beta,beta-caroten-3-ol / 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 / 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 / Photosystem II reaction center protein Y
Similarity search - Component
Biological speciesThermostichus vulcanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKamada, S. / Nakajima, Y. / Shen, J.-R.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structural insights into the action mechanisms of artificial electron acceptors in photosystem II.
Authors: Kamada, S. / Nakajima, Y. / Shen, J.R.
History
DepositionAug 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 30, 2025Group: Atomic model / Data collection / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_alt_id / _atom_site.label_atom_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.type_symbol / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.value_order / _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
Y: Photosystem II reaction center protein Ycf12
X: Photosystem II reaction center protein X
Z: Photosystem II reaction center protein Z
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
y: Photosystem II reaction center protein Ycf12
x: Photosystem II reaction center protein X
z: Photosystem II reaction center protein Z
R: Photosystem II protein Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)748,842375
Polymers597,32639
Non-polymers151,516336
Water58,3153237
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.018, 229.579, 287.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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

#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) Thermostichus 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) Thermostichus 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) Thermostichus vulcanus (bacteria) / References: UniProt: D0VWR7
#4: Protein Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein


Mass: 38419.941 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermostichus vulcanus (bacteria) / References: UniProt: D0VWR8, photosystem II
#7: Protein Photosystem II reaction center protein H / PSII-H


Mass: 7057.349 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermostichus 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) Thermostichus vulcanus (bacteria) / References: UniProt: P12240
#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) Thermostichus 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) Thermostichus 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) Thermostichus 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) Thermostichus vulcanus (bacteria) / References: UniProt: P12312
#13: Protein Photosystem II manganese-stabilizing polypeptide / MSP / Extrinsic protein O of oxygen-evolving complex


Mass: 26651.707 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermostichus 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) Thermostichus 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) Thermostichus vulcanus (bacteria) / References: UniProt: P56152
#17: 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) Thermostichus vulcanus (bacteria) / References: UniProt: D0VWR3
#18: 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) Thermostichus vulcanus (bacteria) / References: UniProt: D0VWR4
#19: Protein Photosystem II reaction center protein Z / PSII-Z


Mass: 6794.197 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermostichus vulcanus (bacteria) / References: UniProt: D0VWR5
#20: Protein/peptide Photosystem II protein Y


Mass: 4590.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermostichus vulcanus (bacteria) / Strain: NIES-2133 / IAM M-273 / BP-1 / References: UniProt: Q8DKM3

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

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


Mass: 9449.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermostichus 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) Thermostichus 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 / Extrinsic protein V of oxygen-evolving complex


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

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Sugars , 3 types, 47 molecules

#29: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#36: 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.: 21 / Source method: obtained synthetically / Formula: C13H26O5S / Comment: detergent*YM
#39: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 21 types, 3526 molecules

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


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


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#23: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 893.489 Da / Num. of mol.: 70 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#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.: 20 / Source method: obtained synthetically / Formula: C40H56
#27: 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
#28: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C45H86O10
#30: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: C3H8O3
#31: Chemical...
ChemComp-UNL / UNKNOWN LIGAND


Mass: 258.120 Da / Num. of mol.: 57 / Source method: obtained synthetically
#32: Chemical ChemComp-K3C / 2-phenylcyclohexa-2,5-diene-1,4-dione


Mass: 184.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H8O2 / Feature type: SUBJECT OF INVESTIGATION
#33: 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 / Feature type: SUBJECT OF INVESTIGATION
#34: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION
#35: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#37: 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
#38: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#40: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#41: Chemical ChemComp-RRX / (3R)-beta,beta-caroten-3-ol / beta-Cryptoxanthin


Mass: 552.872 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56O
#42: Chemical ChemComp-MG / MAGNESIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 3237 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY
Sequence detailsSEQUENCE ABOUT PRO A(A) 279, LEU K(K) 33, TRP K(K) 39 AND LEU M(M) 8, THE AUTHOR CONFIRMED BY ...SEQUENCE 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. THESE RESIDUES OF CHAIN C(C) ARE BASED ON THE DATABASE SEQUENCE FROM THERMOSYNECHOCOCCUS ELONGATUS Q8DIF8_THEEBS

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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: 3.33 Å3/Da / Density % sol: 63.1 %
Crystal growTemperature: 285 K / Method: microbatch / pH: 6.1
Details: 5% PEG1450, 20mM NaCl, 10mM CaCl2, 40mM MgSO4, 20mM MES buffer, pH 6.1, MICRO-BATCH METHOD UNDER OIL, temperature 285K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 13, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 583631 / % possible obs: 98.7 % / Redundancy: 7 % / Biso Wilson estimate: 37.38 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.061 / Net I/σ(I): 18.6
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 7 % / Rmerge(I) obs: 1.465 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 57320 / CC1/2: 0.704 / % possible all: 97.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
MOLREPphasing
REFMAC5.8.0258refinement
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3wu2

3wu2


Resolution: 1.95→49.22 Å / SU ML: 0.2101 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5739
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1814 29246 5.01 %
Rwork0.1526 553946 -
obs0.154 583192 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.07 Å2
Refinement stepCycle: LAST / Resolution: 1.95→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41111 0 10377 3237 54725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008253559
X-RAY DIFFRACTIONf_angle_d1.214273178
X-RAY DIFFRACTIONf_chiral_restr0.05667375
X-RAY DIFFRACTIONf_plane_restr0.00668419
X-RAY DIFFRACTIONf_dihedral_angle_d24.803621150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.970.37259800.369117981X-RAY DIFFRACTION96.94
1.97-20.34229570.327318193X-RAY DIFFRACTION97.88
2-2.020.328410100.303718145X-RAY DIFFRACTION98.08
2.02-2.050.30339750.279718185X-RAY DIFFRACTION98.02
2.05-2.070.2939510.26318258X-RAY DIFFRACTION98.04
2.07-2.10.27279780.248218249X-RAY DIFFRACTION98.19
2.1-2.130.27459230.236418257X-RAY DIFFRACTION98.2
2.13-2.160.26049750.224318244X-RAY DIFFRACTION98.34
2.16-2.20.23399310.203518355X-RAY DIFFRACTION98.42
2.2-2.230.23459310.191518321X-RAY DIFFRACTION98.36
2.23-2.270.22919340.186118371X-RAY DIFFRACTION98.54
2.27-2.310.21539590.170318366X-RAY DIFFRACTION98.57
2.31-2.360.20739950.166318315X-RAY DIFFRACTION98.57
2.36-2.40.21049380.159718375X-RAY DIFFRACTION98.62
2.4-2.460.19339580.151918424X-RAY DIFFRACTION98.74
2.46-2.510.18239820.143318435X-RAY DIFFRACTION98.81
2.51-2.580.18839830.14318410X-RAY DIFFRACTION98.85
2.58-2.650.17879770.13718446X-RAY DIFFRACTION98.97
2.65-2.720.172310020.13618457X-RAY DIFFRACTION98.98
2.72-2.810.18369930.135818569X-RAY DIFFRACTION99.1
2.81-2.910.17559600.130318478X-RAY DIFFRACTION99.07
2.91-3.030.17299760.135818578X-RAY DIFFRACTION99.19
3.03-3.170.17519690.137218631X-RAY DIFFRACTION99.34
3.17-3.330.159310080.133118582X-RAY DIFFRACTION99.29
3.33-3.540.161110010.13318648X-RAY DIFFRACTION99.37
3.54-3.820.16229620.130318675X-RAY DIFFRACTION99.32
3.82-4.20.15069850.125218751X-RAY DIFFRACTION99.47
4.2-4.810.133910130.117418845X-RAY DIFFRACTION99.53
4.81-6.060.156810050.134618972X-RAY DIFFRACTION99.59
6.06-49.220.192110350.176419430X-RAY DIFFRACTION99.42

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