7D0T

Structure of the CYP102A1 Haem Domain with N-Carboxybenzyl-L-Prolyl-L-Phenylalanine in complex with (S)-1-Indanylamine


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-Indanylamine
Crystal Properties
Matthews coefficientSolvent content
2.6553.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.575α = 90
b = 128.074β = 90
c = 147.889γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225-HS2019-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B21.0000SPring-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
11.7449.399.50.2060.2130.0550.99911.314.9114259
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)
11.741.7798.52.9043.0050.7680.5161.115

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 REPLACEMENTTHROUGHOUT5XA31.7448.45108486568599.440.20040.19910.2259RANDOM23.961
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]
-1.311.8-0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.08
r_dihedral_angle_4_deg16.381
r_dihedral_angle_3_deg14.326
r_dihedral_angle_1_deg6.921
r_angle_refined_deg1.628
r_angle_other_deg1.378
r_chiral_restr0.084
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_gen_planes_other0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.08
r_dihedral_angle_4_deg16.381
r_dihedral_angle_3_deg14.326
r_dihedral_angle_1_deg6.921
r_angle_refined_deg1.628
r_angle_other_deg1.378
r_chiral_restr0.084
r_bond_refined_d0.01
r_gen_planes_refined0.008
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 Atoms572
Heterogen Atoms218

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction