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Cytochrome P450-153 from Novosphingobium aromaticivorans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RWL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 0.1 M Hepes, 10% w/v PEG8000
Crystal Properties Matthews coefficient Solvent content 2.65 53.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.133 α = 90 b = 113.133 β = 90 c = 72.97 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 2M 2017-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.966000 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.9 97.98 98.7 0.061 0.947 12.6 3.2 22850
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 2.9 3.08 99.6 0.604 0.745 2.4 3.3
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 3RWL 2.9 97.98 21675 1142 98.59 0.24989 0.24755 0.2546 0.29883 0.3057 RANDOM 69.49
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] -1.55 -0.78 -1.55 5.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.126 r_dihedral_angle_3_deg 21.737 r_dihedral_angle_4_deg 15.531 r_long_range_B_other 10.822 r_long_range_B_refined 10.819 r_dihedral_angle_1_deg 7.927 r_mcangle_it 7.735 r_mcangle_other 7.735 r_scangle_other 7.408 r_mcbond_it 4.918
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.126 r_dihedral_angle_3_deg 21.737 r_dihedral_angle_4_deg 15.531 r_long_range_B_other 10.822 r_long_range_B_refined 10.819 r_dihedral_angle_1_deg 7.927 r_mcangle_it 7.735 r_mcangle_other 7.735 r_scangle_other 7.408 r_mcbond_it 4.918 r_mcbond_other 4.917 r_scbond_it 4.729 r_scbond_other 4.726 r_angle_refined_deg 1.368 r_angle_other_deg 0.835 r_chiral_restr 0.061 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5582 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing