7WY3

Structure of the Oxomolybdenum Mesoporphyrin IX-Reconstituted CYP102A1 F87V Mutant Haem Domain with N-(5-Cyclohexyl)valeroyl-L-Phenylalanine in complex with Styrene


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3WSP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE293PEG8000, Magnesium Chloride, Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.6854.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.67α = 90
b = 128.38β = 90
c = 148.64γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 X 6M2020-12-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL45XU1.00000SPring-8BL45XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.648.581000.1360.1440.9988.089.79414846131.613
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.641002.0792.190.5541.239.912

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3WSP1.648.58141021744099.980.15020.14780.1959RANDOM30.556
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.20.71-0.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.91
r_dihedral_angle_4_deg15.129
r_dihedral_angle_3_deg12.45
r_dihedral_angle_1_deg6.561
r_rigid_bond_restr2.17
r_angle_refined_deg1.453
r_angle_other_deg1.354
r_chiral_restr0.077
r_bond_refined_d0.007
r_gen_planes_refined0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.91
r_dihedral_angle_4_deg15.129
r_dihedral_angle_3_deg12.45
r_dihedral_angle_1_deg6.561
r_rigid_bond_restr2.17
r_angle_refined_deg1.453
r_angle_other_deg1.354
r_chiral_restr0.077
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7320
Nucleic Acid Atoms
Solvent Atoms488
Heterogen Atoms250

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing