7W97

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZO9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE2939%(w/v) PEG8000, 59 mM Magnesium Chloride, 74 mM Tris-HCl, 128 uM N-Hexadecanoyl-L-Homoserine, 1.3%(v/v) Methanol
Crystal Properties
Matthews coefficientSolvent content
2.5551.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.677α = 90
b = 145.51β = 97.27
c = 62.934γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-02-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.000000SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim 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
11.448.51000.060.0650.024119.67.5204864
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.421001.2241.3170.4830.5617.4

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 REPLACEMENTTHROUGHOUT1ZO91.445.591946741013999.960.15890.15790.1767RANDOM18.219
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]
-0.57-0.39-0.040.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.687
r_dihedral_angle_4_deg16.16
r_dihedral_angle_3_deg11.506
r_dihedral_angle_1_deg6.399
r_angle_refined_deg1.597
r_angle_other_deg1.487
r_chiral_restr0.084
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.687
r_dihedral_angle_4_deg16.16
r_dihedral_angle_3_deg11.506
r_dihedral_angle_1_deg6.399
r_angle_refined_deg1.597
r_angle_other_deg1.487
r_chiral_restr0.084
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7294
Nucleic Acid Atoms
Solvent Atoms844
Heterogen Atoms234

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction