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- PDB-4cas: Serial femtosecond crystallography structure of a photosynthetic ... -

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Basic information

Entry
Database: PDB / ID: 4cas
TitleSerial femtosecond crystallography structure of a photosynthetic reaction center
Components
  • (REACTION CENTER PROTEIN ...) x 3
  • PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT
KeywordsPHOTOSYNTHESIS / LIPIDIC-SPONGE PHASE / REACTION CENTER / ELECTRON TRANSPORT / CELL MEMBRANE / METAL- BINDING / TRANSMEMBRANE / CHROMOPHORE
Function / homology
Function and homology information


plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / : / photosynthesis / electron transfer activity / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosynthetic Reaction Center, subunit C; domain 2 / Photosynthetic Reaction Center, subunit C, domain 2 / Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Multiheme cytochrome c family profile. ...Photosynthetic Reaction Center, subunit C; domain 2 / Photosynthetic Reaction Center, subunit C, domain 2 / Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Multiheme cytochrome c family profile. / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / Multiheme cytochrome superfamily / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Few Secondary Structures / Irregular / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN B / DIACYL GLYCEROL / : / HEME C / Chem-MPG / MENAQUINONE-7 / 15-cis-1,2-dihydroneurosporene / Chem-OTP / PHOSPHATE ION ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN B / DIACYL GLYCEROL / : / HEME C / Chem-MPG / MENAQUINONE-7 / 15-cis-1,2-dihydroneurosporene / Chem-OTP / PHOSPHATE ION / Reaction center protein H chain / Reaction center protein L chain / Reaction center protein M chain / Photosynthetic reaction center cytochrome c subunit
Similarity search - Component
Biological speciesBLASTOCHLORIS VIRIDIS (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsJohansson, L.C. / Arnlund, D. / Katona, G. / White, T.A. / Barty, A. / DePonte, D.P. / Shoeman, R.L. / Wickstrand, C. / Sharma, A. / Williams, G.J. ...Johansson, L.C. / Arnlund, D. / Katona, G. / White, T.A. / Barty, A. / DePonte, D.P. / Shoeman, R.L. / Wickstrand, C. / Sharma, A. / Williams, G.J. / Aquila, A. / Bogan, M.J. / Caleman, C. / Davidsson, J. / Doak, R.B. / Frank, M. / Fromme, R. / Galli, L. / Grotjohann, I. / Hunter, M.S. / Kassemeyer, S. / Kirian, R.A. / Kupitz, C. / Liang, M. / Lomb, L. / Malmerberg, E. / Martin, A.V. / Messerschmidt, M. / Nass, K. / Redecke, L. / Seibert, M.M. / Sjohamn, J. / Steinbrener, J. / Stellato, F. / Wang, D. / Wahlgren, W.Y. / Weierstall, U. / Westenhoff, S. / Zatsepin, N.A. / Boutet, S. / Spence, J.C.H. / Schlichting, I. / Chapman, H.N. / Fromme, P. / Neutze, R.
CitationJournal: Nat Commun / Year: 2013
Title: Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography.
Authors: Johansson, L.C. / Arnlund, D. / Katona, G. / White, T.A. / Barty, A. / DePonte, D.P. / Shoeman, R.L. / Wickstrand, C. / Sharma, A. / Williams, G.J. / Aquila, A. / Bogan, M.J. / Caleman, C. / ...Authors: Johansson, L.C. / Arnlund, D. / Katona, G. / White, T.A. / Barty, A. / DePonte, D.P. / Shoeman, R.L. / Wickstrand, C. / Sharma, A. / Williams, G.J. / Aquila, A. / Bogan, M.J. / Caleman, C. / Davidsson, J. / Doak, R.B. / Frank, M. / Fromme, R. / Galli, L. / Grotjohann, I. / Hunter, M.S. / Kassemeyer, S. / Kirian, R.A. / Kupitz, C. / Liang, M. / Lomb, L. / Malmerberg, E. / Martin, A.V. / Messerschmidt, M. / Nass, K. / Redecke, L. / Seibert, M.M. / Sjohamn, J. / Steinbrener, J. / Stellato, F. / Wang, D. / Wahlgren, W.Y. / Weierstall, U. / Westenhoff, S. / Zatsepin, N.A. / Boutet, S. / Spence, J.C. / Schlichting, I. / Chapman, H.N. / Fromme, P. / Neutze, R.
History
DepositionOct 9, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: Database references
Revision 2.0Jun 14, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conf / struct_conn / struct_conn_type / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _struct_conn_type.id / _struct_site.details / _struct_site.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_id
Revision 2.1Nov 15, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_site / _diffrn_source.pdbx_wavelength_list ..._diffrn_source.pdbx_synchrotron_site / _diffrn_source.pdbx_wavelength_list / _diffrn_source.source / _diffrn_source.type
Revision 2.2Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author / diffrn_detector
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _diffrn_detector.detector / _diffrn_detector.type
Revision 2.3Nov 14, 2018Group: Data collection / Category: diffrn / Item: _diffrn.pdbx_serial_crystal_experiment
Revision 3.0Jan 23, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_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.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_asym.entity_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_comp_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_id
Revision 3.1Sep 4, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_CC_half / _reflns.pdbx_R_split ..._reflns.pdbx_CC_half / _reflns.pdbx_R_split / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_netI_over_sigmaI / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_R_split
Revision 3.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT
B: REACTION CENTER PROTEIN L CHAIN
C: REACTION CENTER PROTEIN M CHAIN
D: REACTION CENTER PROTEIN H CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,38824
Polymers134,6404
Non-polymers11,74820
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area48640 Å2
ΔGint-366.2 kcal/mol
Surface area40640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.900, 84.800, 384.300
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 , 1 types, 1 molecules A

#1: Protein PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT / CYTOCHROME C558/C559


Mass: 39419.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: DEUTSCHE SAMMLUNG VON MIKROORGANISMEN UND ZELLKULTUREN GMBH (DSMZ)
Source: (natural) BLASTOCHLORIS VIRIDIS (bacteria) / References: UniProt: P07173

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REACTION CENTER PROTEIN ... , 3 types, 3 molecules BCD

#2: Protein REACTION CENTER PROTEIN L CHAIN / PHOTOSYNTHETIC REACTION CENTER L SUBUNIT


Mass: 30600.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: DEUTSCHE SAMMLUNG VON MIKROORGANISMEN UND ZELLKULTUREN GMBH (DSMZ)
Source: (natural) BLASTOCHLORIS VIRIDIS (bacteria) / References: UniProt: P06009
#3: Protein REACTION CENTER PROTEIN M CHAIN / PHOTOSYNTHETIC REACTION CENTER M SUBUNIT


Mass: 36063.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: DEUTSCHE SAMMLUNG VON MIKROORGANISMEN UND ZELLKULTUREN GMBH (DSMZ)
Source: (natural) BLASTOCHLORIS VIRIDIS (bacteria) / References: UniProt: P06010
#4: Protein REACTION CENTER PROTEIN H CHAIN / PHOTOSYNTHETIC REACTION CENTER H SUBUNIT


Mass: 28557.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: DEUTSCHE SAMMLUNG VON MIKROORGANISMEN UND ZELLKULTUREN GMBH (DSMZ)
Source: (natural) BLASTOCHLORIS VIRIDIS (bacteria) / References: UniProt: P06008

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Non-polymers , 10 types, 20 molecules

#5: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#6: Chemical ChemComp-DGA / DIACYL GLYCEROL


Mass: 625.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H76O5
#7: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#8: Chemical ChemComp-BPB / BACTERIOPHEOPHYTIN B


Mass: 887.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H74N4O6
#9: Chemical ChemComp-MPG / [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#10: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#11: Chemical ChemComp-MQ7 / MENAQUINONE-7


Mass: 648.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H64O2
#12: Chemical ChemComp-NS5 / 15-cis-1,2-dihydroneurosporene


Mass: 540.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H60
#13: Chemical ChemComp-OTP / (2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL TRIHYDROGEN DIPHOSPHATE / OCTAPRENYL PYROPHOSPHATE


Mass: 722.911 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H68O7P2
#14: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1175

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Sample preparation

CrystalDensity Matthews: 3.49 Å3/Da / Density % sol: 64.8 %
Description: DATA WAS COLLECTED ON 1175 MICROCRYSTALS AT THE LCLS USING THE SERIAL FEMTOSECOND CRYSTALLOGRAPHY METHOD.
Crystal growpH: 8.1
Details: BATCH CRYSTALLIZATIONS WERE SET UP IN SEPTUM-SEALED GLASS VIALS CONTAINING 100 UL PROTEIN (30-35 MG/ML), 100 UL LIPIDIC SPONGE PHASE (12 % MONOOLEIN, 17.5 % JEFFAMINE M 600, 1.0 M HEPES PH 8. ...Details: BATCH CRYSTALLIZATIONS WERE SET UP IN SEPTUM-SEALED GLASS VIALS CONTAINING 100 UL PROTEIN (30-35 MG/ML), 100 UL LIPIDIC SPONGE PHASE (12 % MONOOLEIN, 17.5 % JEFFAMINE M 600, 1.0 M HEPES PH 8.0, 0.7 M (NH4)2SO4, 2.5 % 1,2,3- HEPTANETRIOL) AND 100 UL 1.0-1.2 M TRI-SODIUM CITRATE

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.32 / Wavelength: 1.32 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Feb 19, 2011 / Details: BE LENSES
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.32 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. obs: 23496 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 27 % / CC1/2: 0.54 / R split: 0.365 / Net I/σ(I): 3.5
Reflection shellResolution: 3.5→3.59 Å / Redundancy: 26.6 % / Mean I/σ(I) obs: 2 / CC1/2: 0.32 / R split: 0.527 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WJN

2wjn


Resolution: 3.5→49.64 Å / Cor.coef. Fo:Fc: 0.731 / Cor.coef. Fo:Fc free: 0.645 / SU B: 86.357 / SU ML: 0.737 / Cross valid method: THROUGHOUT / ESU R Free: 0.763 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.32903 1264 5.1 %RANDOM
Rwork0.29461 ---
obs0.29639 23496 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.177 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å20 Å20 Å2
2--0.84 Å20 Å2
3----2.76 Å2
Refinement stepCycle: LAST / Resolution: 3.5→49.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9076 0 805 0 9881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0210281
X-RAY DIFFRACTIONr_bond_other_d0.0010.029554
X-RAY DIFFRACTIONr_angle_refined_deg1.9742.03114098
X-RAY DIFFRACTIONr_angle_other_deg1.0953.00121811
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.58351170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.42722.411394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.713151304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7271556
X-RAY DIFFRACTIONr_chiral_restr0.0780.21439
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111532
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022533
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9012.1574683
X-RAY DIFFRACTIONr_mcbond_other0.9012.1574682
X-RAY DIFFRACTIONr_mcangle_it1.5713.2325846
X-RAY DIFFRACTIONr_mcangle_other1.5713.2325847
X-RAY DIFFRACTIONr_scbond_it1.4662.6025598
X-RAY DIFFRACTIONr_scbond_other1.4562.5955591
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.143.7958239
X-RAY DIFFRACTIONr_long_range_B_refined4.55921.63940412
X-RAY DIFFRACTIONr_long_range_B_other4.55821.6440413
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.5→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 86 -
Rwork0.29 1725 -
obs--99.61 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6155-0.4114-0.00791.233-0.53151.5874-0.06680.04820.1625-0.07930.18120.0297-0.1965-0.0842-0.11450.09-0.0728-0.00040.1403-0.00850.1721-5.620829.988-88.9271
20.15970.4156-0.0481.8955-0.10463.35390.0941-0.1466-0.08770.6029-0.06070.03190.23330.0031-0.03340.22990.02220.07220.37710.06260.2702-6.47811.1541-45.695
30.74710.10310.23471.275-0.05941.9737-0.0014-0.17330.10770.58050.1079-0.0653-0.29980.1646-0.10660.3197-0.0173-0.06790.24270.03760.25887.622526.6645-46.0864
40.9330.5624-0.56081.0492-0.54832.57270.138-0.3276-0.07330.8976-0.1445-0.22380.1674-0.05810.00651.0894-0.0522-0.140.57790.03360.3496-2.803412.4851-19.2398
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 332
2X-RAY DIFFRACTION2B1 - 273
3X-RAY DIFFRACTION3C1 - 323
4X-RAY DIFFRACTION4D1 - 258

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