7W9J

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6K58 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE2778.5%(w/v)PEG8000, 60 mM Magnesium Chloride, 75 mM Tris-HCl, 250 uM N-Dodecanoyl-L-Homoserine Lactone, 1%(v/v) Methanol
Crystal Properties
Matthews coefficientSolvent content
2.5251.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.295α = 90
b = 121.827β = 90
c = 148.689γ = 90
Symmetry
Space GroupP 21 21 21

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
11.7549.6399.10.1430.1540.9989.297.10910724230.641
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)
11.751.85971.411.5270.5811.476.727

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 REPLACEMENTTHROUGHOUT6K581.7549.63101500532999.360.17970.17810.2099RANDOM27.511
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]
-1.152.13-0.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.108
r_dihedral_angle_4_deg14.714
r_dihedral_angle_3_deg12.704
r_dihedral_angle_1_deg6.482
r_angle_refined_deg1.403
r_angle_other_deg1.336
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_deg32.108
r_dihedral_angle_4_deg14.714
r_dihedral_angle_3_deg12.704
r_dihedral_angle_1_deg6.482
r_angle_refined_deg1.403
r_angle_other_deg1.336
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 Atoms7335
Nucleic Acid Atoms
Solvent Atoms428
Heterogen Atoms146

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction