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Cytochrome P460 from Methyloccocus capsulatus in the ferrous state (single crosslink from Lys)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HIU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 2 uL of 7 mg/mL protein with 2 uL precipitant 1.9 M ammonium sulfate, 100 mM Tris-HCl pH 8.0
Cryoprotectant 1.0 M sodium malonate final, soak 100 mM sodium hydrosulfite final
Crystal Properties Matthews coefficient Solvent content 2.51 51.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.38 α = 90 b = 80.441 β = 90 c = 84.78 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 100 PIXEL DECTRIS EIGER X 9M Mirrors 2024-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.6199 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.33 58.34 100 0.122 0.133 0.052 0.998 8.9 6.4 73519
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.33 1.35 99 2.112 2.407 1.133 0.228 4.2
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 1.33 58.34 69671 3735 99.82 0.1584 0.1562 0.1655 0.19976 0.2027 RANDOM 19.131
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] 0.23 -2.23 2
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 16.293 r_long_range_B_other 13.589 r_dihedral_angle_3_deg 12.401 r_dihedral_angle_2_deg 6.849 r_scangle_other 6.746 r_dihedral_angle_1_deg 6.412 r_mcangle_other 5.786 r_mcangle_it 5.784 r_scbond_it 4.697 r_scbond_other 4.697
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 16.293 r_long_range_B_other 13.589 r_dihedral_angle_3_deg 12.401 r_dihedral_angle_2_deg 6.849 r_scangle_other 6.746 r_dihedral_angle_1_deg 6.412 r_mcangle_other 5.786 r_mcangle_it 5.784 r_scbond_it 4.697 r_scbond_other 4.697 r_mcbond_it 3.853 r_mcbond_other 3.84 r_rigid_bond_restr 3.055 r_angle_refined_deg 2.074 r_angle_other_deg 0.63 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2200 Nucleic Acid Atoms Solvent Atoms 404 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement DIALS data scaling DIALS data reduction REFMAC phasing