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Structure of the CYP102A1 Haem Domain with N-(S)-Ibuprofenoyl-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 293 PEG8000, Magnesium Chloride, Tris-HCl, 0.5% DMSO, 150 uM N-(S)-Ibuprofenoyl-L-Phenylalanine
Crystal Properties Matthews coefficient Solvent content 2.68 54.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.898 α = 90 b = 148.806 β = 98.12 c = 64.691 γ = 90
Symmetry Space Group P 1 21 1
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 2018-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.00000 SPring-8 BL32XU
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 2.1 48.54 100 0.135 0.145 0.055 0.998 9.5 6.9 64121
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 2.1 2.15 100 1.867 2.014 0.749 0.515 1 7.2
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 2.1 46.55 60945 3142 99.91 0.1945 0.1921 0.1989 0.2408 0.2445 RANDOM 40.697
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] -0.05 0.08 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.152 r_dihedral_angle_3_deg 15.639 r_dihedral_angle_4_deg 15.491 r_dihedral_angle_1_deg 6.903 r_angle_refined_deg 1.542 r_angle_other_deg 1.29 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.152 r_dihedral_angle_3_deg 15.639 r_dihedral_angle_4_deg 15.491 r_dihedral_angle_1_deg 6.903 r_angle_refined_deg 1.542 r_angle_other_deg 1.29 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7312 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 164
Software Software Software Name Purpose XDS data reduction Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction