7CKN

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


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-{2-[4-(Trifluoromethoxy)phenoxy]}acetoyl-L-Phenylalanine, 500 uM Isopropylamine
Crystal Properties
Matthews coefficientSolvent content
2.6854.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.666α = 90
b = 128.425β = 90
c = 148.694γ = 90
Symmetry
Space GroupP 21 21 21

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 BL26B11.000SPring-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
11.5548.61000.1010.1050.0290.99915.213.4163294
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)
11.551.581002.1612.2420.5940.50714.2

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 REPLACEMENTTHROUGHOUT5XA31.5548.6155023815699.940.15180.14940.1985RANDOM24.478
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]
-0.070.08-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.131
r_dihedral_angle_4_deg17.348
r_dihedral_angle_3_deg13.941
r_dihedral_angle_1_deg6.874
r_rigid_bond_restr4.414
r_angle_refined_deg1.914
r_angle_other_deg1.551
r_chiral_restr0.108
r_bond_refined_d0.015
r_gen_planes_refined0.012
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.131
r_dihedral_angle_4_deg17.348
r_dihedral_angle_3_deg13.941
r_dihedral_angle_1_deg6.874
r_rigid_bond_restr4.414
r_angle_refined_deg1.914
r_angle_other_deg1.551
r_chiral_restr0.108
r_bond_refined_d0.015
r_gen_planes_refined0.012
r_gen_planes_other0.006
r_bond_other_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7328
Nucleic Acid Atoms
Solvent Atoms661
Heterogen Atoms288

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction