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- PDB-1s5l: Architecture of the photosynthetic oxygen evolving center -

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Basic information

Entry
Database: PDB / ID: 1s5l
TitleArchitecture of the photosynthetic oxygen evolving center
Components
  • (Cytochrome b559 ...) x 2
  • (Photosystem II ...) x 15
  • Cytochrome c-550
  • Photosystem Q(B) protein
KeywordsPHOTOSYNTHESIS / photosystem / oxygen-evolving / tetra-manganese / membrane
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 / 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 / Single helix bin ...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 / Single helix bin / 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 PsbX, type 1 subfamily / 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 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 / 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 / : / HEME C / OXYGEN EVOLVING SYSTEM / PHEOPHYTIN A / Chem-PL9 / Photosystem II extrinsic protein V / Photosystem II extrinsic protein O ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / : / HEME C / OXYGEN EVOLVING SYSTEM / PHEOPHYTIN A / Chem-PL9 / Photosystem II extrinsic protein V / Photosystem II extrinsic protein O / 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 / Photosystem II reaction center protein X
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.5 Å
AuthorsFerreira, K.N. / Iverson, T.M. / Maghlaoui, K. / Barber, J. / Iwata, S.
CitationJournal: Science / Year: 2004
Title: Architecture of the Photosynthetic Oxygen-Evolving Center
Authors: Ferreira, K.N. / Iverson, T.M. / Maghlaoui, K. / Barber, J. / Iwata, S.
History
DepositionJan 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 25, 2012Group: Non-polymer description
Revision 2.0Mar 3, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
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.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 3.0Dec 25, 2024Group: Advisory / Data collection ...Advisory / 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_validate_chiral / pdbx_validate_close_contact / struct_conn
Item: _chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE Because the electron density for the two N chains was poor, the authors were unable to ...SEQUENCE Because the electron density for the two N chains was poor, the authors were unable to assign side chains.
Remark 600HETEROGEN Ligand PL9 is missing two isoprenoids due to disorder in the electron density.

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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: photosystem II core light harvesting 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 PsbH 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 PsbT protein
U: Photosystem II 12 kDa extrinsic protein
V: Cytochrome c-550
X: photosystem II PsbX protein
N: Photosystem II PsbN protein
Z: Photosystem II reaction center Z protein
a: Photosystem Q(B) protein
b: photosystem II core light harvesting 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 PsbH 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 PsbT protein
u: Photosystem II 12 kDa extrinsic protein
v: Cytochrome c-550
x: photosystem II PsbX protein
n: Photosystem II PsbN protein
z: Photosystem II reaction center Z protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)692,750146
Polymers609,92238
Non-polymers82,828108
Water00
1
A: Photosystem Q(B) protein
B: photosystem II core light harvesting 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 PsbH 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 PsbT protein
U: Photosystem II 12 kDa extrinsic protein
V: Cytochrome c-550
X: photosystem II PsbX protein
N: Photosystem II PsbN protein
Z: Photosystem II reaction center Z protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)346,37573
Polymers304,96119
Non-polymers41,41454
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
a: Photosystem Q(B) protein
b: photosystem II core light harvesting 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 PsbH 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 PsbT protein
u: Photosystem II 12 kDa extrinsic protein
v: Cytochrome c-550
x: photosystem II PsbX protein
n: Photosystem II PsbN protein
z: Photosystem II reaction center Z protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)346,37573
Polymers304,96119
Non-polymers41,41454
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.992, 228.849, 309.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsthe biological unit is a dimer, which is present in the asymmetric unit

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Components

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Protein , 2 types, 4 molecules AaVv

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


Mass: 38265.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: P0A444
#16: Protein Cytochrome c-550 / 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

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

#2: Protein photosystem II core light harvesting protein


Mass: 56656.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q8DIQ1
#3: Protein photosystem II CP43 protein


Mass: 51666.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q8DIF8
#4: Protein photosystem II reaction center D2 protein


Mass: 39388.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q8CM25
#7: Protein photosystem II PsbH protein


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 / 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


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 / 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 / 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 / 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 / MSP


Mass: 26851.965 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 PsbT protein


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 / PS II complex 12 kDa extrinsic protein / PSII-U


Mass: 15030.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q9F1L5
#17: Protein/peptide photosystem II PsbX protein


Mass: 5235.296 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q9F1R6
#18: Protein/peptide Photosystem II PsbN protein


Mass: 3166.895 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria)
#19: Protein Photosystem II reaction center Z protein / photosystem II PsbZ protein


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 / 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 / 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 , 1 types, 2 molecules

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


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 8 types, 106 molecules

#20: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#21: Chemical
ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CHO3
#22: Chemical ChemComp-OEC / OXYGEN EVOLVING SYSTEM


Mass: 323.828 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O4
#23: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 72 / 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-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
#27: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C40H56
#28: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4

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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: 1

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Sample preparation

CrystalDensity Matthews: 3.92 Å3/Da / Density % sol: 68.64 %
Crystal growTemperature: 291 K / Method: pseudo-batch hanging drop / pH: 7.5
Details: 100mM HEPES, 100mM (NH4)2SO4, PEG 4000, C12E8, trimethyl lead acetate, pH 7.5, pseudo-batch hanging drop, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.75 mg/mlchlorophyll1drop
220 mMMES1droppH6.5
310 mM1dropCaCl2
410 mM1dropMgCl2
5100 mMHEPES1reservoirpH7.5
6100 mMammonium sulfate1reservoir
720 %glycerol1reservoir
88.0-14.0 %PEG40001reservoir
90.11 mM1reservoirC12E8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 25, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. all: 117866 / Num. obs: 103604 / % possible obs: 87.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.5→3.52 Å / % possible all: 80.9
Reflection
*PLUS
Lowest resolution: 40 Å / % possible obs: 87.3 % / Redundancy: 2.88 % / Num. measured all: 298731 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 80.9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
RefinementMethod to determine structure: MIR / Resolution: 3.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.342 981 random
Rwork0.296 --
obs0.296 101219 -
all-101219 -
Refinement stepCycle: LAST / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39991 0 5954 0 45945
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.96
X-RAY DIFFRACTIONc_bond_d0.014
Refinement
*PLUS
Num. reflection all: 103485 / % reflection Rfree: 1 % / Rfactor Rfree: 0.346 / Rfactor Rwork: 0.303
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2.11
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.04
LS refinement shell
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 3.56 Å / Rfactor Rfree: 0.384 / Rfactor Rwork: 0.34

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

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