7CX6

Structure of the CYP102A1 Haem Domain with N-(5-Cyclohexyl)valeroyl-L-Phenylalanine in complex with (R)-(+)-1-Phenylethylamine


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-(5-Cyclohexyl)valeroyl-L-phenylalanine, 1 mM (R)-(+)-1-Phenylethylamine
Crystal Properties
Matthews coefficientSolvent content
2.652.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.56α = 90
b = 146.113β = 100.04
c = 64.624γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2019-07-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B11.0000SPring-8BL26B1

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
11.6948.799.50.1080.1170.0440.99912.87.1118525
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)
11.691.7296.51.5791.7210.6730.5311.16.4

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 REPLACEMENTTHROUGHOUT5XA31.6948.03112617586599.40.16820.16670.198RANDOM22.575
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]
-1.45-0.33-0.061.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.005
r_dihedral_angle_4_deg17.554
r_dihedral_angle_3_deg13.441
r_dihedral_angle_1_deg6.637
r_angle_refined_deg1.481
r_angle_other_deg1.386
r_chiral_restr0.076
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_gen_planes_other0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.005
r_dihedral_angle_4_deg17.554
r_dihedral_angle_3_deg13.441
r_dihedral_angle_1_deg6.637
r_angle_refined_deg1.481
r_angle_other_deg1.386
r_chiral_restr0.076
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 Atoms7335
Nucleic Acid Atoms
Solvent Atoms648
Heterogen Atoms268

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction