☰ Navigation Tabs
Structure of the CYP102A1 Haem Domain with N-Carboxybenzyl-L-Prolyl-L-Phenylalanine in complex with Cyclohexylamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XA3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 293 PEG 8000, Magnesium Chloride, Tris-HCl, 0.5 % DMSO, 200 uM N-Carboxybenzyl-L-Prolyl-L-Phenylalanine, 500 uM Cyclohexylamine
Crystal Properties Matthews coefficient Solvent content 2.7 54.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.82 α = 90 b = 128.83 β = 90 c = 149.33 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 9M 2019-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.000 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.49 48.82 100 0.111 0.116 0.999 10.78 11.415 176109 27.88
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.49 1.53 100 2.31 2.416 0.52 1 11.644
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5XA3 1.49 48.82 176109 9220 99.95 0.1409 0.139 0.1393 0.1777 0.1783 RANDOM 23.457
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] -0.18 0.56 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.125 r_dihedral_angle_4_deg 14.118 r_dihedral_angle_3_deg 13.096 r_dihedral_angle_1_deg 6.423 r_rigid_bond_restr 1.795 r_angle_refined_deg 1.522 r_angle_other_deg 1.441 r_chiral_restr 0.084 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.125 r_dihedral_angle_4_deg 14.118 r_dihedral_angle_3_deg 13.096 r_dihedral_angle_1_deg 6.423 r_rigid_bond_restr 1.795 r_angle_refined_deg 1.522 r_angle_other_deg 1.441 r_chiral_restr 0.084 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7328 Nucleic Acid Atoms Solvent Atoms 890 Heterogen Atoms 286
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing PDB_EXTRACT data extraction