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Architectural insights into spatially distinct corrin and metal binding sites of CobN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9FPC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 273 0.2M Lithium sulfate, 30% PEG 4000, 0.1M Tris pH 8.5.
Crystal Properties Matthews coefficient Solvent content 2.36 47.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.32 α = 90 b = 73.6 β = 90 c = 86.47 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 PILATUS 6M 2013-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.58 56.05 99.6 0.067 18.6 18.6 13012
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.58 2.65 0.559 2.3
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 2.58 56.05 12341 630 99.55 0.18789 0.1836 0.1892 0.27526 0.2774 RANDOM 64.068
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] 0.06 -0.01 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.277 r_long_range_B_refined 13.23 r_long_range_B_other 13.228 r_dihedral_angle_2_deg 12.525 r_scangle_other 11.186 r_mcangle_it 8.393 r_mcangle_other 8.392 r_scbond_it 7.595 r_scbond_other 7.588 r_dihedral_angle_1_deg 6.956
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.277 r_long_range_B_refined 13.23 r_long_range_B_other 13.228 r_dihedral_angle_2_deg 12.525 r_scangle_other 11.186 r_mcangle_it 8.393 r_mcangle_other 8.392 r_scbond_it 7.595 r_scbond_other 7.588 r_dihedral_angle_1_deg 6.956 r_mcbond_it 6.101 r_mcbond_other 6.099 r_angle_refined_deg 1.733 r_angle_other_deg 0.602 r_chiral_restr 0.084 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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 3030 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing