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Structure of the CYP102A1 Haem Domain with N-Enanthyl-L-Prolyl-L-Phenylalanine
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 277 PEG 8000, Magnesium Chloride, Tris-HCl, 0.5% DMSO, 200 uM N-Enanthyl-L-Prolyl-L-Phenylalanine
Crystal Properties Matthews coefficient Solvent content 2.68 54.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.055 α = 90 b = 126.769 β = 90 c = 149 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 16M 2019-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.99999 SPring-8 BL41XU
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 1.41 48.32 100 0.065 0.067 0.018 1 17.1 13.4 215305
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 1.41 1.43 99.9 2.227 2.337 0.702 0.687 1 10.8
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 1.41 48.32 204485 10702 99.95 0.1463 0.1447 0.1451 0.1776 0.1777 RANDOM 22.196
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] -0.2 0.19 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.056 r_dihedral_angle_4_deg 16.09 r_dihedral_angle_3_deg 12.644 r_dihedral_angle_1_deg 6.552 r_rigid_bond_restr 2.282 r_angle_refined_deg 1.629 r_angle_other_deg 1.486 r_chiral_restr 0.092 r_bond_refined_d 0.01 r_gen_planes_refined 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.056 r_dihedral_angle_4_deg 16.09 r_dihedral_angle_3_deg 12.644 r_dihedral_angle_1_deg 6.552 r_rigid_bond_restr 2.282 r_angle_refined_deg 1.629 r_angle_other_deg 1.486 r_chiral_restr 0.092 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7335 Nucleic Acid Atoms Solvent Atoms 877 Heterogen Atoms 340
Software Software Software Name Purpose XDS data reduction Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction