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Crystal Structure Analysis of the cytochrome P450 CYP-Sb21
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NWS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 277 BIS-TRIS, PEG 8000, Ca-acetate
Crystal Properties Matthews coefficient Solvent content 2.18 43.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.636 α = 90 b = 91.092 β = 94.65 c = 52.975 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 SIEMENS-NICOLET mirrors 2018-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.976 SSRF 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 1.85 52.8 99.4 0.066 0.072 0.027 7.3 6.7 33433
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 1.85 1.88 99.2 0.532 0.578 0.224 0.902 6.4
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 5NWS 1.85 50 30220 1658 94.62 0.1534 0.1509 0.1626 0.1974 0.2072 RANDOM 23.702
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] -0.15 0.07 -0.34 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.445 r_dihedral_angle_4_deg 16.507 r_dihedral_angle_3_deg 13.637 r_dihedral_angle_1_deg 6.029 r_angle_refined_deg 1.958 r_angle_other_deg 1.146 r_chiral_restr 0.125 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 r_gen_planes_other 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.445 r_dihedral_angle_4_deg 16.507 r_dihedral_angle_3_deg 13.637 r_dihedral_angle_1_deg 6.029 r_angle_refined_deg 1.958 r_angle_other_deg 1.146 r_chiral_restr 0.125 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 r_gen_planes_other 0.007 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3038 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-3000 data reduction REFMAC phasing