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Structure of the CYP102A1 Haem Domain with N-enanthyl-L-prolyl-L-phenylalanine in complex with Ethylamine
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-enanthyl-L-prolyl-L-phenylalanine, 0.5 mM Ethylamine
Crystal Properties Matthews coefficient Solvent content 2.7 54.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.897 α = 90 b = 128.581 β = 90 c = 148.938 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 1.0000 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 1.68 48.66 99.9 0.189 0.205 0.998 10.59 6.965 249765 33.367
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 1.68 1.78 99.5 1.958 2.13 0.537 1.03 6.481
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 48.66 123286 6500 99.92 0.1872 0.1857 0.1946 0.214 0.2221 RANDOM 27.794
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] -0.19 0.95 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.178 r_dihedral_angle_4_deg 15.411 r_dihedral_angle_3_deg 13 r_dihedral_angle_1_deg 6.761 r_angle_refined_deg 1.69 r_angle_other_deg 1.432 r_chiral_restr 0.089 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.178 r_dihedral_angle_4_deg 15.411 r_dihedral_angle_3_deg 13 r_dihedral_angle_1_deg 6.761 r_angle_refined_deg 1.69 r_angle_other_deg 1.432 r_chiral_restr 0.089 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7328 Nucleic Acid Atoms Solvent Atoms 562 Heterogen Atoms 287
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction