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Cytochrome P460 from Methyloccocus capsulatus (double crosslink from Lys), aged
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SFX structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 100 nL protein at 7 mg/mL with 100 nL of precipitant (2.05 M ammonium sulfate, 100 mM Tris-HCl pH 8.0)
Crystal Properties Matthews coefficient Solvent content 2.55 51.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.701 α = 90 b = 80.468 β = 90 c = 84.612 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 PIXEL DECTRIS EIGER2 X 4M 2023-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE VMXi 0.7749 Diamond VMXi
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim 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 1.77 58.32 99.31 0.1479 0.982 15.88 66.5 31820
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.833 0.285 0.54
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 1.77 58.32 30324 1498 99.99 0.14648 0.14421 0.1524 0.19437 0.1973 RANDOM 35.021
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] 0.28 -0.62 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.314 r_dihedral_angle_2_deg 13.439 r_long_range_B_refined 9.611 r_long_range_B_other 9.589 r_scangle_other 6.96 r_dihedral_angle_1_deg 6.854 r_scbond_it 4.871 r_scbond_other 4.851 r_mcangle_it 4.689 r_mcangle_other 4.688
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.314 r_dihedral_angle_2_deg 13.439 r_long_range_B_refined 9.611 r_long_range_B_other 9.589 r_scangle_other 6.96 r_dihedral_angle_1_deg 6.854 r_scbond_it 4.871 r_scbond_other 4.851 r_mcangle_it 4.689 r_mcangle_other 4.688 r_mcbond_it 3.518 r_mcbond_other 3.484 r_angle_refined_deg 2.264 r_angle_other_deg 0.815 r_chiral_restr 0.129 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 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 2200 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement DIALS data scaling DIALS data reduction REFMAC phasing