7E46

Structure of the CYP102A1 Haem Domain with N-Carboxybenzyl-L-Prolyl-L-Phenylalanine in complex with (S)-(-)-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-Carboxybenzyl-L-Prolyl-L-Phenylalanine, 1 mM (S)-(-)-1-Phenylethylamine
Crystal Properties
Matthews coefficientSolvent content
2.6954.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.855α = 90
b = 128.428β = 90
c = 148.81γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2019-07-25MSINGLE 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
11.9148.611000.2030.2120.060.9989.812.388352
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)
11.911.941002.2282.3360.6840.5081.411.1

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 REPLACEMENTTHROUGHOUT5XA31.9148.6183889435699.920.23470.23280.2705RANDOM26.366
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]
-1.161.54-0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.192
r_dihedral_angle_3_deg15.59
r_dihedral_angle_4_deg15.303
r_dihedral_angle_1_deg7.298
r_angle_refined_deg1.623
r_angle_other_deg1.293
r_chiral_restr0.081
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_gen_planes_other0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.192
r_dihedral_angle_3_deg15.59
r_dihedral_angle_4_deg15.303
r_dihedral_angle_1_deg7.298
r_angle_refined_deg1.623
r_angle_other_deg1.293
r_chiral_restr0.081
r_bond_refined_d0.009
r_gen_planes_refined0.008
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 Atoms455
Heterogen Atoms168

Software

Software
Software NamePurpose
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction