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Basic information

Entry
Database: PDB / ID: 1jb0
TitleCrystal Structure of Photosystem I: a Photosynthetic Reaction Center and Core Antenna System from Cyanobacteria
Components
  • (PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT ...) x 8
  • (PHOTOSYSTEM I ...) x 4
KeywordsPHOTOSYNTHESIS / MEMBRANE PROTEIN / MULTIPROTEIN-PIGMENT COMPLEX
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / protein-chromophore linkage / electron transfer activity ...photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / protein-chromophore linkage / electron transfer activity / magnesium ion binding / integral component of membrane / metal ion binding
Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I PsaA/PsaB, conserved site / Electron transport accessory-like domain superfamily / Photosystem I PsaM, reaction centre / Photosystem I PsaX / Photosystem I protein PsaC / Photosystem I PsaK, reaction centre / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / Photosystem I, reaction centre subunit XI ...Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I PsaA/PsaB, conserved site / Electron transport accessory-like domain superfamily / Photosystem I PsaM, reaction centre / Photosystem I PsaX / Photosystem I protein PsaC / Photosystem I PsaK, reaction centre / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / Photosystem I, reaction centre subunit XI / Photosystem I PsaA / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaX superfamily / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaA/PsaB superfamily / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I PsaB / Photosystem I PsaL, reaction centre subunit XI / Photosystem I reaction centre subunit PsaK / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaE, reaction centre subunit IV / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit VIII / Photosystem I PsaA/PsaB / Photosystem I PsaG/PsaK protein / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaD / Photosystem I PsaK, reaction centre / Alpha-t-alpha / Photosystem I PsaL, reaction centre subunit XI / Photosystem 1 Reaction Centre Subunit Xi; Chain: L; / Photosystem I, reaction centre, subunit PsaF / Photosystem I p700 chlorophyll A apoprotein A1 / Photosystem 1 Reaction Centre Subunit Ii; Chain: D; / Photosystem I PsaA/PsaB / Photosystem I PsaD, reaction center subunit II / Single helix bin / SH3 type barrels. - #50 / Alpha-Beta Plaits - #20 / Helicase, Ruva Protein; domain 3 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / SH3 type barrels. / Roll / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Photosystem I 4.8K protein / Photosystem I reaction center subunit III / Photosystem I iron-sulfur center / Photosystem I reaction center subunit XII / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit II / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit PsaK / Photosystem I reaction center subunit VIII ...Photosystem I 4.8K protein / Photosystem I reaction center subunit III / Photosystem I iron-sulfur center / Photosystem I reaction center subunit XII / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit II / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit PsaK / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit II / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit PsaK / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit III / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit XII / Photosystem I P700 chlorophyll a apoprotein A1
Biological speciesSynechococcus elongatus (Cyanobacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsJordan, P. / Fromme, P. / Witt, H.T. / Klukas, O. / Saenger, W. / Krauss, N.
Citation
Journal: NATURE / Year: 2001
Title: Three-dimensional Structure of Cyanobacterial Photosystem I at 2.5 A Resolution
Authors: Jordan, P. / Fromme, P. / Witt, H.T. / Klukas, O. / Saenger, W. / Krauss, N.
#1: Journal: J.Biol.Chem. / Year: 1999
Title: PHOTOSYSTEM I, AN IMPROVED MODEL OF THE STROMAL SUBUNITS PSAC, PSAD AND PSAE
Authors: Klukas, O. / Schubert, W.D. / Jordan, P. / Krauss, N. / Fromme, P. / Witt, H.T. / Saenger, W.
#2: Journal: J.Biol.Chem. / Year: 1999
Title: LOCALISATION OF TWO PHYLLOQUINONES, QK AND QK', IN AN IMPROVED ELECTRON DENSITY MAP OF PHOTOSYSTEM I AT 4-A RESOLUTION
Authors: Klukas, O. / Schubert, W.D. / Jordan, P. / Krau, N. / Fromme, P. / Witt, H.T. / Saenger, W.
#3: Journal: J.Mol.Biol. / Year: 1997
Title: PHOTOSYSTEM I OF SYNECHOCOCCUS ELONGATUS AT 4 A RESOLUTION: COMPREHENSIVE STRUCTURE ANALYSIS
Authors: Schubert, W.D. / Klukas, O. / Krauss, N. / Saenger, W. / Fromme, P. / Witt, H.T.
#4: Journal: Nat.Struct.Biol. / Year: 1996
Title: PHOTOSYSTEM I AT 4 A RESOLUTION REPRESENTS THE FIRST STRUCTURAL MODEL OF A JOINT PHOTOSYNTHETIC REACTION CENTRE AND CORE ANTENNA SYSTEM
Authors: Krauss, N. / Schubert, W.D. / Klukas, O. / Fromme, P. / Witt, H.T. / Saenger, W.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJun 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 25, 2012Group: Non-polymer description
Revision 1.4May 11, 2016Group: Derived calculations
Revision 1.5Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.6Nov 20, 2019Group: Advisory / Database references / Derived calculations
Category: database_PDB_caveat / pdbx_struct_conn_angle ...database_PDB_caveat / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A1
B: PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A2
C: PHOTOSYSTEM I IRON-SULFUR CENTER
D: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT II
E: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT IV
F: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT III
I: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT VIII
J: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT IX
K: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT X
L: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT XI
M: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT XII
X: PHOTOSYSTEM I SUBUNIT PSAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)359,700140
Polymers257,16212
Non-polymers102,539128
Water3,621201
1
A: PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A1
B: PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A2
C: PHOTOSYSTEM I IRON-SULFUR CENTER
D: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT II
E: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT IV
F: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT III
I: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT VIII
J: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT IX
K: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT X
L: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT XI
M: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT XII
X: PHOTOSYSTEM I SUBUNIT PSAX
hetero molecules

A: PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A1
B: PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A2
C: PHOTOSYSTEM I IRON-SULFUR CENTER
D: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT II
E: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT IV
F: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT III
I: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT VIII
J: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT IX
K: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT X
L: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT XI
M: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT XII
X: PHOTOSYSTEM I SUBUNIT PSAX
hetero molecules

A: PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A1
B: PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A2
C: PHOTOSYSTEM I IRON-SULFUR CENTER
D: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT II
E: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT IV
F: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT III
I: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT VIII
J: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT IX
K: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT X
L: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT XI
M: PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT XII
X: PHOTOSYSTEM I SUBUNIT PSAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,079,100420
Polymers771,48536
Non-polymers307,616384
Water54030
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Unit cell
γ
α
β
Length a, b, c (Å)281.000, 281.000, 165.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11L-4042-

HOH

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Components

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PHOTOSYSTEM I ... , 4 types, 4 molecules ABCX

#1: Protein PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A1 / / PHOTOSYSTEM I SUBUNIT PSAA


Mass: 83267.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (Cyanobacteria) / References: UniProt: P25896, UniProt: P0A405*PLUS
#2: Protein PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A2 / / PHOTOSYSTEM I SUBUNIT PSAB


Mass: 82992.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (Cyanobacteria) / References: UniProt: P25897, UniProt: P0A407*PLUS
#3: Protein PHOTOSYSTEM I IRON-SULFUR CENTER / / PHOTOSYSTEM I SUBUNIT PSAC


Mass: 8678.011 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (Cyanobacteria) / References: UniProt: P18083, UniProt: P0A415*PLUS
#12: Protein/peptide PHOTOSYSTEM I SUBUNIT PSAX /


Mass: 3845.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (Cyanobacteria) / References: UniProt: Q8DKP6*PLUS

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PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT ... , 8 types, 8 molecules DEFIJKLM

#4: Protein PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT II / PHOTOSYSTEM I SUBUNIT PSAD


Mass: 15258.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (Cyanobacteria) / References: UniProt: P20452, UniProt: P0A420*PLUS
#5: Protein PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT IV / PHOTOSYSTEM I SUBUNIT PSAE


Mass: 8268.290 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (Cyanobacteria) / References: UniProt: P25898, UniProt: P0A423*PLUS
#6: Protein PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT III / PHOTOSYSTEM I SUBUNIT PSAF


Mass: 17716.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (Cyanobacteria) / References: UniProt: P25899, UniProt: P0A401*PLUS
#7: Protein/peptide PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT VIII / PHOTOSYSTEM I SUBUNIT PSAI


Mass: 4297.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (Cyanobacteria) / References: UniProt: P25900, UniProt: P0A427*PLUS
#8: Protein/peptide PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT IX / PHOTOSYSTEM I SUBUNIT PSAJ


Mass: 4770.698 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (Cyanobacteria) / References: UniProt: P25901, UniProt: P0A429*PLUS
#9: Protein PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT X / PHOTOSYSTEM I SUBUNIT PSAK


Mass: 8483.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (Cyanobacteria) / References: UniProt: P20453, UniProt: P0A425*PLUS
#10: Protein PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT XI / PHOTOSYSTEM I SUBUNIT PSAL


Mass: 16156.569 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (Cyanobacteria) / References: UniProt: P25902, UniProt: Q8DGB4*PLUS
#11: Protein/peptide PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT XII / PHOTOSYSTEM I SUBUNIT PSAM


Mass: 3426.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (Cyanobacteria) / References: UniProt: P25903, UniProt: P0A403*PLUS

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Non-polymers , 8 types, 329 molecules

#13: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 96 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#14: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE / Phytomenadione


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2
#15: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#16: Chemical...
ChemComp-BCR / BETA-CAROTENE / Beta-Carotene


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


Mass: 722.970 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#18: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H86O10
#19: Chemical ChemComp-CA / CALCIUM ION / Calcium


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#20: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O

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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: 7.32 Å3/Da / Density % sol: 83.2 %
Crystal growTemperature: 277 K / Method: microdialysis / pH: 6.4
Details: beta-dodecylmaltoside, magnesium sulfate, pH 6.4, MICRODIALYSIS, temperature 277K
Crystal grow
*PLUS
Method: batch method
Details: Fromme, P., (1998) Biochim. Biophys. Acta, 1365, 175.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mM11MgSO4
21 mMchlorophyll11

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineDiffraction-IDWavelength (Å)
SYNCHROTRONESRF ID210.99
SYNCHROTRONESRF ID220.99
Detector
TypeDiffraction-IDDetectorDate
MARRESEARCH1IMAGE PLATENov 20, 1998
MARRESEARCH2IMAGE PLATENov 20, 1998
Radiation
Diffraction-IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 246961 / Num. obs: 246961 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 48 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 14
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 2.9 / Num. unique all: 22495 / % possible all: 88.9
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 88.9 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS0.9refinement
RefinementMethod to determine structure: MIR / Resolution: 2.5→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.217 4743 -random
Rwork0.199 ---
All0.199 233377 --
Obs0.199 233377 93.3 %-
Solvent computationSolvent model: BULK SOLVENT CORRECTION HAS BEEN APPLIED IN CNS
Displacement parametersBiso mean: 46.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.29 Å
Luzzati sigma a0.37 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17394 0 6603 201 24198
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.547
X-RAY DIFFRACTIONc_dihedral_angle_d19.61
X-RAY DIFFRACTIONc_improper_angle_d1.29
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefinement-IDNum. reflection obs
2.5-2.520.287570.2963476X-RAY DIFFRACTION3533
2.52-2.530.29820.282X-RAY DIFFRACTION4107
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.61
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.29
LS refinement shell
*PLUS
Rfactor Rfree: 0.287 / Rfactor Rwork: 0.296

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