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Structure of the CYP102A1 Haem Domain with N-(5-Cyclohexyl)valeroyl-L-Phenylalanine in complex with (R)-1-Indanylamine
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-(5-Cyclohexyl)valeroyl-L-phenylalanine, 1 mM (R)-1-Indanylamine
Crystal Properties Matthews coefficient Solvent content 2.66 53.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.709 α = 90 b = 128.236 β = 90 c = 147.812 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 CCD RAYONIX MX225-HS 2019-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.000 SPring-8 BL26B2
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.68 48.43 100 0.187 0.194 0.05 0.999 13.1 14.9 127789
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) Redundancy Number Unique Reflections (All) 1 1.68 1.71 100 2.969 3.075 0.794 0.524 14.8
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 1.68 48.43 121307 6386 99.96 0.1843 0.1828 0.1921 0.2127 0.2185 RANDOM 21.251
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] -1.2 1.35 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.459 r_dihedral_angle_4_deg 15.228 r_dihedral_angle_3_deg 13.945 r_dihedral_angle_1_deg 6.784 r_angle_refined_deg 1.717 r_angle_other_deg 1.45 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.459 r_dihedral_angle_4_deg 15.228 r_dihedral_angle_3_deg 13.945 r_dihedral_angle_1_deg 6.784 r_angle_refined_deg 1.717 r_angle_other_deg 1.45 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7328 Nucleic Acid Atoms Solvent Atoms 677 Heterogen Atoms 366
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction