7COO

Structure of the CYP102A1 Haem Domain with N-Carboxybenzyl-L-Prolyl-L-Phenylalanine in complex with Cyclohexylamine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5XA3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE293PEG 8000, Magnesium Chloride, Tris-HCl, 0.5 % DMSO, 200 uM N-Carboxybenzyl-L-Prolyl-L-Phenylalanine, 500 uM Cyclohexylamine
Crystal Properties
Matthews coefficientSolvent content
2.754.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.82α = 90
b = 128.83β = 90
c = 149.33γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2019-10-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL32XU1.000SPring-8BL32XU

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
11.4948.821000.1110.1160.99910.7811.41517610927.88
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)
11.491.531002.312.4160.52111.644

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 REPLACEMENTTHROUGHOUT5XA31.4948.82176109922099.950.14090.1390.1777RANDOM23.457
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]
-0.180.56-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.125
r_dihedral_angle_4_deg14.118
r_dihedral_angle_3_deg13.096
r_dihedral_angle_1_deg6.423
r_rigid_bond_restr1.795
r_angle_refined_deg1.522
r_angle_other_deg1.441
r_chiral_restr0.084
r_bond_refined_d0.007
r_gen_planes_refined0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.125
r_dihedral_angle_4_deg14.118
r_dihedral_angle_3_deg13.096
r_dihedral_angle_1_deg6.423
r_rigid_bond_restr1.795
r_angle_refined_deg1.522
r_angle_other_deg1.441
r_chiral_restr0.084
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7328
Nucleic Acid Atoms
Solvent Atoms890
Heterogen Atoms286

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction