7D1F

Structure of the CYP102A1 Haem Domain with N-enanthyl-L-prolyl-L-phenylalanine in complex with Methylamine


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-Enanthyl-L-prolyl-L-phenylalanine, 500 uM Methylamine
Crystal Properties
Matthews coefficientSolvent content
2.6353.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.474α = 90
b = 127.338β = 90
c = 147.759γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225-HS2019-07-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B21.000SPring-8BL26B2

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
11.4548.2399.30.0720.0750.02119.714.4193978
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)
11.451.4790.32.0472.150.6420.5541.310.6

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 REPLACEMENTTHROUGHOUT5XA31.4548.23184213966699.170.14440.14290.174RANDOM22.736
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]
-0.631.18-0.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.488
r_dihedral_angle_4_deg17.265
r_dihedral_angle_3_deg12.24
r_dihedral_angle_1_deg6.575
r_rigid_bond_restr1.824
r_angle_refined_deg1.566
r_angle_other_deg1.422
r_chiral_restr0.086
r_bond_refined_d0.009
r_gen_planes_refined0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.488
r_dihedral_angle_4_deg17.265
r_dihedral_angle_3_deg12.24
r_dihedral_angle_1_deg6.575
r_rigid_bond_restr1.824
r_angle_refined_deg1.566
r_angle_other_deg1.422
r_chiral_restr0.086
r_bond_refined_d0.009
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 Atoms7328
Nucleic Acid Atoms
Solvent Atoms613
Heterogen Atoms352

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction