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Cytochrome P450 monooxygenase from Streptomyces scabiei (SscaCYP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WIY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289.15 0.2 M magnesium formate dihydrate, 20% w/v polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.43 49.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.27 α = 90 b = 46.89 β = 90 c = 75.73 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 PIXEL DECTRIS PILATUS3 6M 2023-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9999 Diamond I24
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 1.48 47.38 100 0.154 0.168 0.998 9.82 12.3 139161
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.48 1.52 2.238 2.636 0.19899999999999998
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.48 47.38 69236 3596 99.98 0.16539 0.16416 0.1627 0.18918 0.1869 RANDOM 19.95
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] -0.35 1.32 -0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.105 r_dihedral_angle_2_deg 8.135 r_dihedral_angle_1_deg 5.814 r_long_range_B_refined 5.596 r_long_range_B_other 5.521 r_scangle_other 5.119 r_scbond_it 3.435 r_scbond_other 3.435 r_mcangle_other 2.419 r_mcangle_it 2.415
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.105 r_dihedral_angle_2_deg 8.135 r_dihedral_angle_1_deg 5.814 r_long_range_B_refined 5.596 r_long_range_B_other 5.521 r_scangle_other 5.119 r_scbond_it 3.435 r_scbond_other 3.435 r_mcangle_other 2.419 r_mcangle_it 2.415 r_angle_refined_deg 1.764 r_mcbond_it 1.741 r_mcbond_other 1.726 r_angle_other_deg 0.584 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_gen_planes_other 0.004 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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 3046 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling xia2 data reduction BALBES phasing Coot model building