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Cytochrome P460 from Methyloccocus capsulatus (double crosslink from Lys)
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 2 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 Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.657 α = 90 b = 80.627 β = 90 c = 84.695 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 2023-08-10 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 1.66 58.39 99.72 0.0846 0.999 18.92 80.5 38507
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 1.66 1.719 97.35 0.428 33.7
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 1.66 58.39 36644 1872 99.99 0.14424 0.14224 0.151 0.18324 0.1855 RANDOM 30.178
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] 0.53 -0.72 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.501 r_dihedral_angle_2_deg 13.881 r_long_range_B_refined 9.029 r_long_range_B_other 9.017 r_dihedral_angle_1_deg 6.723 r_scangle_other 6.214 r_scbond_it 4.222 r_scbond_other 4.195 r_mcangle_it 4.092 r_mcangle_other 4.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.501 r_dihedral_angle_2_deg 13.881 r_long_range_B_refined 9.029 r_long_range_B_other 9.017 r_dihedral_angle_1_deg 6.723 r_scangle_other 6.214 r_scbond_it 4.222 r_scbond_other 4.195 r_mcangle_it 4.092 r_mcangle_other 4.091 r_mcbond_it 3.038 r_mcbond_other 2.999 r_angle_refined_deg 2.211 r_angle_other_deg 0.81 r_chiral_restr 0.13 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 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 2284 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement DIALS data scaling DIALS data reduction REFMAC phasing