7W9D

Crystal Structure of the Oxomolybdenum Mesoporphyrin IX-Reconstituted CYP102A1 (P450BM3) Heme Domain with N-Hexadecanoyl-L-Homoserine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7W97 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE2777.8%(w/v) PEG8000, 60 mM Magnesium Chloride, 74 mM Tris-HCl, 150 uM N-Hexadecanoyl-L-Homoserine, 1.5%(v/v) Methanol
Crystal Properties
Matthews coefficientSolvent content
2.5652.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.754α = 90
b = 146.716β = 98.04
c = 62.854γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2021-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL45XU1.000000SPring-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
11.5547.599.20.0790.0880.99812.015.05215201228.149
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)
11.551.6497.20.9421.0490.6271.565.158

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 REPLACEMENTTHROUGHOUT7W971.5547.5143959745899.560.1690.16810.1859RANDOM22.59
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]
-0.47-0.33-0.270.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.022
r_dihedral_angle_4_deg16.155
r_dihedral_angle_3_deg11.658
r_dihedral_angle_1_deg6.483
r_angle_refined_deg1.421
r_angle_other_deg1.395
r_chiral_restr0.076
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.022
r_dihedral_angle_4_deg16.155
r_dihedral_angle_3_deg11.658
r_dihedral_angle_1_deg6.483
r_angle_refined_deg1.421
r_angle_other_deg1.395
r_chiral_restr0.076
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7328
Nucleic Acid Atoms
Solvent Atoms564
Heterogen Atoms162

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction