☰ Navigation Tabs
The surface-exposed lipo-protein of BtuG2 in complex with hydroxycobalamin.
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 7.8 298 50 mM TRIS pH 7.8, 100 mM NaCl, 20 mM MgCl, 10 mM hydroxycobalamin, 33 % PEG4000
Crystal Properties Matthews coefficient Solvent content 2.59 52.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.11 α = 90 b = 101.099 β = 97.81 c = 79.893 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 0.9677 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 1.5 79.16 99.2 0.97 18.5 8 123287
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 1.5 7.4 0.95
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 FREE R-VALUE 6FFV 1.5 62.4 112532 5900 96.1 0.1446 0.143 0.1464 0.1745 0.1769 RANDOM 15.922
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] 2.89 1.22 -2.79 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.512 r_dihedral_angle_1_deg 7.601 r_dihedral_angle_2_deg 7.507 r_rigid_bond_restr 5.698 r_angle_refined_deg 1.936 r_mcbond_it 1.357 r_mcangle_it 1.149 r_mcbond_other 0.893 r_angle_other_deg 0.581 r_chiral_restr 0.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.512 r_dihedral_angle_1_deg 7.601 r_dihedral_angle_2_deg 7.507 r_rigid_bond_restr 5.698 r_angle_refined_deg 1.936 r_mcbond_it 1.357 r_mcangle_it 1.149 r_mcbond_other 0.893 r_angle_other_deg 0.581 r_chiral_restr 0.274 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5247 Nucleic Acid Atoms Solvent Atoms 508 Heterogen Atoms 360
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing