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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 in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 0.1 M Bis-Tris propane HCl, pH 7.0, 1.4 M sodium malonate
Crystal Properties Matthews coefficient Solvent content 2.96 58.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.724 α = 90 b = 145.391 β = 90 c = 116.382 γ = 90
Symmetry Space Group C 2 2 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 2021-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8731 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 1.95 45.43 93.24 0.9 14.2 7.5 30854
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 1.95 2.02 0.82
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 1.95 45.43 29323 1531 93.26 0.23749 0.23523 0.2418 0.28125 0.2829 RANDOM 30.968
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] 1.98 -0.96 -1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.128 r_long_range_B_refined 8.909 r_dihedral_angle_1_deg 7.742 r_dihedral_angle_2_deg 7.139 r_scbond_it 4.165 r_mcangle_it 3.706 r_mcbond_it 2.575 r_angle_refined_deg 2.527 r_chiral_restr 0.184 r_bond_refined_d 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.128 r_long_range_B_refined 8.909 r_dihedral_angle_1_deg 7.742 r_dihedral_angle_2_deg 7.139 r_scbond_it 4.165 r_mcangle_it 3.706 r_mcbond_it 2.575 r_angle_refined_deg 2.527 r_chiral_restr 0.184 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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 2652 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction PHASER phasing