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- PDB-2axt: Crystal Structure of Photosystem II from Thermosynechococcus elongatus -

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Basic information

Entry
Database: PDB / ID: 2axt
TitleCrystal Structure of Photosystem II from Thermosynechococcus elongatus
Components
  • (Cytochrome b559 ...) x 2
  • (Photosystem II ...) x 12
  • CP47 protein
  • Cytochrome c-550
  • Photosystem Q(B) protein
  • Unassigned subunits
KeywordsELECTRON TRANSPORT / photosystem / ps ii / ps2 / membrane complex / transmembrane alpha-helix
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 / extrinsic component of membrane ...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 / extrinsic component of membrane / response to herbicide / : / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthetic electron transport in photosystem II / phosphate ion binding / photosynthesis, light reaction / photosynthesis / respiratory electron transport chain / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
photosynthetic oxygen evolving center fold / photosynthetic oxygen evolving center domain / Photosystem II, cytochrome c-550 precursor / Photosystem II 12 kDa extrinsic protein / Photosystem II reaction center protein H / photosystem ii from thermosynechococcus elongatus / Photosystem II PsbZ, reaction centre / Photosystem II CP47 reaction center protein / Photosystem II CP47 reaction center protein / Photosystem II cytochrome b559, alpha subunit ...photosynthetic oxygen evolving center fold / photosynthetic oxygen evolving center domain / Photosystem II, cytochrome c-550 precursor / Photosystem II 12 kDa extrinsic protein / Photosystem II reaction center protein H / photosystem ii from thermosynechococcus elongatus / 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 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 / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / 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 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 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 reaction centre protein H superfamily / 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 / Photosystem II 10 kDa phosphoprotein / 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 / Porin / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / : / 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 / Arc Repressor Mutant, subunit A / Roll / Up-down Bundle / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Chem-MGE / OXYGEN EVOLVING SYSTEM / PHEOPHYTIN A ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Chem-MGE / OXYGEN EVOLVING SYSTEM / PHEOPHYTIN A / Chem-PQ9 / Chem-SQD / Unknown ligand / : / : / : / Photosystem II extrinsic protein V / Photosystem II extrinsic protein O / Photosystem II protein D1 1 / Photosystem II protein D1 1 / Photosystem II reaction center protein J / Photosystem II D2 protein / Photosystem II reaction center protein M / Photosystem II reaction center protein Z / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein L / Cytochrome b559 subunit beta / Cytochrome b559 subunit alpha / Photosystem II reaction center protein T / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein H / Photosystem II reaction center protein I / Photosystem II reaction center protein K / Photosystem II extrinsic protein U
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3 Å
AuthorsLoll, B. / Kern, J. / Saenger, W. / Zouni, A. / Biesiadka, J.
CitationJournal: NATURE / Year: 2005
Title: Towards complete cofactor arrangement in the 3.0 A resolution structure of photosystem II
Authors: Loll, B. / Kern, J. / Saenger, W. / Zouni, A. / Biesiadka, J.
History
DepositionSep 6, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 2.0Dec 20, 2017Group: Atomic model / Category: atom_site / Item: _atom_site.type_symbol
Revision 3.0Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_site
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 4.0Feb 5, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_site_gen
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)720,871216
Polymers608,50336
Non-polymers112,368180
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.692, 225.403, 306.106
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 8 molecules AaBbVvXx

#1: Protein Photosystem Q(B) protein / Reaction centre subunit D1 / 32 kDa thylakoid membrane protein / Photosystem II protein D1


Mass: 38265.625 Da / Num. of mol.: 2 / Fragment: residues 1-344 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: P0A445, UniProt: P0A444*PLUS
#2: Protein CP47 protein / Antenna subunit CP47


Mass: 56656.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: GenBank: 11761354, UniProt: Q8DIQ1*PLUS
#16: Protein Cytochrome c-550 / Cyt c-550 / subunit PsbV / 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 (bacteria) / References: UniProt: P0A386
#17: Protein Unassigned subunits


Mass: 10996.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria)

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Photosystem II ... , 12 types, 24 molecules CcDdHhIiJjKkLlMmOoTtUuZz

#3: Protein photosystem II CP43 protein / Antenna subunit CP43


Mass: 51666.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: GenBank: 22295356, UniProt: Q8DIF8*PLUS
#4: Protein photosystem II reaction center D2 protein / Reaction centre subunit D2


Mass: 39388.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: GenBank: 22295355, UniProt: Q8CM25*PLUS
#7: Protein Photosystem II reaction center H protein / Subunit PsbH / PSII-H


Mass: 7358.754 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q8DJ43
#8: Protein/peptide Photosystem II reaction center I protein / Subunit PsbI / PSII 4.4 kDa protein


Mass: 4410.245 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q8DJZ6
#9: Protein/peptide Photosystem II reaction center J protein / Subunit PsbJ


Mass: 4105.908 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: P59087
#10: Protein/peptide Photosystem II reaction center protein K / Subunit PsbK / PSII-K


Mass: 4101.911 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q9F1K9
#11: Protein/peptide Photosystem II reaction center L protein / Subunit PsbL / 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 (bacteria) / References: UniProt: Q8DIN8
#12: Protein/peptide Photosystem II reaction center M protein / Subunit PsbM / PSII-M


Mass: 3981.673 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q8DHA7
#13: Protein Photosystem II manganese-stabilizing polypeptide / Subunit PsbO / MSP


Mass: 26923.045 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: P0A431
#14: Protein/peptide Photosystem II reaction center T protein / Subunit PsbT / PSII-T / PSII-Tc


Mass: 3878.728 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q8DIQ0
#15: Protein Photosystem II 12 kDa extrinsic protein / Subunit PsbU / 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 elongatus (bacteria) / References: UniProt: Q9F1L5
#18: Protein Photosystem II reaction center Z protein / Subunit PsbZ


Mass: 6766.187 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q8DHJ2

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

#5: Protein Cytochrome b559 alpha subunit / Cyt b-559 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 elongatus (bacteria) / References: UniProt: Q8DIP0
#6: Protein/peptide Cytochrome b559 beta subunit / Cyt b-559 subunit beta / PSII reaction center subunit VI


Mass: 5067.900 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q8DIN9

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Sugars , 2 types, 14 molecules

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


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#30: 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 , 13 types, 166 molecules

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


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#20: Chemical...
ChemComp-CLA / CHLOROPHYLL A


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


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5
#22: Chemical
ChemComp-PQ9 / 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE


Mass: 612.967 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C43H64O2
#23: Chemical ChemComp-OEC / OXYGEN EVOLVING SYSTEM


Mass: 323.828 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O4
#24: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C40H56
#25: Chemical ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#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.: 6 / Source method: obtained synthetically / Formula: C41H78O12S
#28: Chemical
ChemComp-MGE / (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE / MONOGALACTOSYL-DIACYLGLYCEROL


Mass: 688.972 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C38H72O10
#29: Chemical...
ChemComp-UNL / UNKNOWN LIGAND


Mass: 103.120 Da / Num. of mol.: 34 / Source method: obtained synthetically
#31: Chemical ChemComp-BCT / BICARBONATE ION


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


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.76 Å3/Da / Density % sol: 67.32 %
Crystal growTemperature: 298 K / Method: batch / pH: 7
Details: PEG 2000, PIPES, magnesium chloride, pH 7.0, batch, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 24, 2005
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 155380 / % possible obs: 88.2 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rsym value: 0.103 / Net I/σ(I): 14.83
Reflection shellResolution: 3→3.05 Å / Mean I/σ(I) obs: 2.17 / Rsym value: 0.466 / % possible all: 73.3

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIRAS / Resolution: 3→10 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 4628278.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1620 1.2 %RANDOM
Rwork0.234 ---
obs0.234 129965 75.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.6527 Å2 / ksol: 0.303343 e/Å3
Displacement parametersBiso mean: 71.3 Å2
Baniso -1Baniso -2Baniso -3
1-27.02 Å20 Å20 Å2
2---2.46 Å20 Å2
3----24.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.78 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40684 0 7570 0 48254
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d18.9
X-RAY DIFFRACTIONc_improper_angle_d1.8
X-RAY DIFFRACTIONc_mcbond_it1.071.5
X-RAY DIFFRACTIONc_mcangle_it1.822
X-RAY DIFFRACTIONc_scbond_it2.752
X-RAY DIFFRACTIONc_scangle_it3.522.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3→3.18 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.383 182 1.3 %
Rwork0.343 14106 -
obs--50.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3cof-new2.param
X-RAY DIFFRACTION4water_rep.param

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