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Crystal structure of cytochrome P450mel 107F1 with biaryl coupling reactivity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D09
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 18% v/v 2-Propanol, 0.1 M Sodium citrate tribasic dihydrate pH 5.5, 20% w/v Polyethylene glycol 4000
Crystal Properties Matthews coefficient Solvent content 3.36 63.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.508 α = 90 b = 117.508 β = 90 c = 75.164 γ = 120
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 PILATUS3 S 6M 2018-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NFPSS BEAMLINE BL19U1 0.979 NFPSS BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.5 50 100 0.236 0.242 0.054 3.5 20 7557
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 3.5 3.56 100 0.554 0.567 0.124 0.969 20.9
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 2d09 3.5 42.17 6784 735 99.55 0.1968 0.1882 0.1902 0.2814 0.2755 RANDOM 49.89
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 0.1 0.2 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.845 r_dihedral_angle_3_deg 18.337 r_dihedral_angle_4_deg 17.191 r_dihedral_angle_1_deg 7.72 r_angle_refined_deg 1.679 r_angle_other_deg 1.198 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.845 r_dihedral_angle_3_deg 18.337 r_dihedral_angle_4_deg 17.191 r_dihedral_angle_1_deg 7.72 r_angle_refined_deg 1.679 r_angle_other_deg 1.198 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3133 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PDB_EXTRACT data extraction REFMAC phasing