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The surface-exposed lipo-protein of BtuG2 in complex with cyanocobalamin.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NQG 1NQG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 TRIS pH 8.0, PEG4000, NaCl, MgCl
Crystal Properties Matthews coefficient Solvent content 2.6 52.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.24 α = 89.97 b = 79.936 β = 89.89 c = 101.047 γ = 82.28
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 2021-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.69 101.1 99 0.98 18 6 169723
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 1.69 8.6 0.98
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1NQG 1.69 42.63 162166 1812 96.26 0.15723 0.15699 0.1574 0.18007 0.1834 RANDOM 19.03
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] 0.12 -0.22 0.1 -0.44 -0.02 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.958 r_dihedral_angle_1_deg 7.181 r_dihedral_angle_2_deg 7.019 r_long_range_B_refined 6.793 r_scbond_it 3.756 r_mcangle_it 2.197 r_angle_refined_deg 2.006 r_mcbond_it 1.574 r_chiral_restr 0.132 r_gen_planes_refined 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.958 r_dihedral_angle_1_deg 7.181 r_dihedral_angle_2_deg 7.019 r_long_range_B_refined 6.793 r_scbond_it 3.756 r_mcangle_it 2.197 r_angle_refined_deg 2.006 r_mcbond_it 1.574 r_chiral_restr 0.132 r_gen_planes_refined 0.013 r_bond_refined_d 0.012 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10494 Nucleic Acid Atoms Solvent Atoms 780 Heterogen Atoms 524
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing