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Cytochrome P450 Enzyme AbyV
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ABB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.1 M Bis-Tris pH 7, 25% PEG3350, 0.2 M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.43 49.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.77 α = 90 b = 91.83 β = 92.36 c = 82.55 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 PILATUS 6M-F 2018-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
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 2.01 61.438 99.9 0.078 0.092 0.999 14 6.8 50350
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.01 2.06 100 1.31 0.728 1.5 6.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3ABB 2.01 61.438 50329 2409 99.814 0.193 0.1903 0.1903 0.2383 0.2382 51.391
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] -2.387 0.635 -3.326 5.641
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.742 r_dihedral_angle_3_deg 17.7 r_dihedral_angle_4_deg 16.22 r_lrange_it 8.235 r_lrange_other 8.23 r_dihedral_angle_1_deg 6.49 r_scangle_it 5.976 r_scangle_other 5.976 r_mcangle_it 5.459 r_mcangle_other 5.458
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.742 r_dihedral_angle_3_deg 17.7 r_dihedral_angle_4_deg 16.22 r_lrange_it 8.235 r_lrange_other 8.23 r_dihedral_angle_1_deg 6.49 r_scangle_it 5.976 r_scangle_other 5.976 r_mcangle_it 5.459 r_mcangle_other 5.458 r_scbond_it 3.974 r_scbond_other 3.974 r_mcbond_other 3.786 r_mcbond_it 3.785 r_angle_other_deg 2.326 r_angle_refined_deg 1.587 r_symmetry_nbd_other 0.221 r_nbd_other 0.209 r_nbd_refined 0.205 r_symmetry_nbd_refined 0.181 r_nbtor_refined 0.154 r_xyhbond_nbd_refined 0.148 r_symmetry_xyhbond_nbd_refined 0.13 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.072 r_bond_other_d 0.035 r_gen_planes_other 0.015 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_symmetry_xyhbond_nbd_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5410 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 221
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling