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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 6FFV 6FFV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 50 mM TRIS pH, 100 mM NaCl, 20 mM ZnCl, 20 mM Cyanocobalamin, PEG2000 20%
Crystal Properties Matthews coefficient Solvent content 2.57 52.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.177 α = 90 b = 100.593 β = 97.6 c = 79.579 γ = 90
Symmetry Space Group P 1 21 1
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 2 78.89 99 0.96 14 8 51840
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 2 8 0.94
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6FFV 2 44.199 51786 2531 99.896 0.184 0.181 0.1811 0.2432 0.2435 RANDOM 29.056
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] 4.305 1.984 -3.026 -1.747
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.588 r_dihedral_angle_3_deg 14.227 r_dihedral_angle_2_deg 12.888 r_dihedral_angle_1_deg 7.763 r_rigid_bond_restr 3.988 r_lrange_it 3.824 r_lrange_other 3.823 r_scangle_it 2.817 r_scangle_other 2.817 r_mcangle_it 2.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.588 r_dihedral_angle_3_deg 14.227 r_dihedral_angle_2_deg 12.888 r_dihedral_angle_1_deg 7.763 r_rigid_bond_restr 3.988 r_lrange_it 3.824 r_lrange_other 3.823 r_scangle_it 2.817 r_scangle_other 2.817 r_mcangle_it 2.46 r_mcangle_other 2.46 r_scbond_it 2.068 r_scbond_other 2.068 r_angle_refined_deg 1.806 r_mcbond_it 1.703 r_mcbond_other 1.689 r_angle_other_deg 0.778 r_nbd_other 0.261 r_symmetry_nbd_refined 0.239 r_symmetry_nbd_other 0.176 r_nbtor_refined 0.174 r_nbd_refined 0.168 r_symmetry_xyhbond_nbd_refined 0.149 r_chiral_restr 0.135 r_xyhbond_nbd_refined 0.124 r_symmetry_nbtor_other 0.081 r_ncsr_local_group_1 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5247 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 331
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing