7CZI

Structure of the CYP102A1 Haem Domain with N-{2-[4-(Trifluoromethoxy)phenoxy]}acetoyl-L-Phenylalanine


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, 125 uM N-{2-[4-(Trifluoromethoxy)phenoxy]}acetoyl-L-Phenylalanine
Crystal Properties
Matthews coefficientSolvent content
2.6954.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.752α = 90
b = 128.591β = 90
c = 148.871γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-11-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0000SPring-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
11.6448.71000.1830.1910.0520.9968.513.4138691
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)
11.641.671003.0083.1230.8370.6751.113.8

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 REPLACEMENTTHROUGHOUT5XA31.6448.7131612697099.930.19170.19040.2151RANDOM24.344
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]
0.211.25-1.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.601
r_dihedral_angle_4_deg15.665
r_dihedral_angle_3_deg13.606
r_dihedral_angle_1_deg6.877
r_angle_refined_deg1.654
r_angle_other_deg1.435
r_chiral_restr0.087
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_gen_planes_other0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.601
r_dihedral_angle_4_deg15.665
r_dihedral_angle_3_deg13.606
r_dihedral_angle_1_deg6.877
r_angle_refined_deg1.654
r_angle_other_deg1.435
r_chiral_restr0.087
r_bond_refined_d0.01
r_gen_planes_refined0.009
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 Atoms716
Heterogen Atoms264

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction