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Vibrio cholerae GbpA (LPMO domain)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XWX Truncated after residue 203
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.2 M Zinc Acetate
0.1 M Sodium Cacodylate pH 6.5
18% w/v PEG 8K
Crystal Properties Matthews coefficient Solvent content 2.02 39.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.333 α = 90 b = 89.374 β = 90 c = 47.497 γ = 90
Symmetry Space Group P 21 21 2
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 PILATUS3 2M 2021-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.87313 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 1.62 47.542 99.94 0.998 10.83 6.8 78744
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 1.62 1.68 0.374
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.62 47.542 41528 2034 99.966 0.178 0.1763 0.1864 0.213 0.2211 25.413
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] -1.884 0.881 1.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.756 r_dihedral_angle_3_deg 14.295 r_lrange_other 8.791 r_lrange_it 8.784 r_dihedral_angle_1_deg 8.297 r_scangle_it 7.199 r_scangle_other 7.198 r_dihedral_angle_2_deg 6.085 r_scbond_it 4.998 r_scbond_other 4.997
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.756 r_dihedral_angle_3_deg 14.295 r_lrange_other 8.791 r_lrange_it 8.784 r_dihedral_angle_1_deg 8.297 r_scangle_it 7.199 r_scangle_other 7.198 r_dihedral_angle_2_deg 6.085 r_scbond_it 4.998 r_scbond_other 4.997 r_mcangle_it 4.32 r_mcangle_other 4.319 r_mcbond_it 3.409 r_mcbond_other 3.326 r_angle_refined_deg 1.341 r_angle_other_deg 0.461 r_symmetry_nbd_refined 0.354 r_nbd_other 0.32 r_nbd_refined 0.228 r_symmetry_nbd_other 0.208 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.167 r_symmetry_xyhbond_nbd_refined 0.149 r_metal_ion_refined 0.126 r_symmetry_metal_ion_refined 0.125 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.071 r_symmetry_xyhbond_nbd_other 0.061 r_gen_planes_refined 0.016 r_bond_refined_d 0.006 r_gen_planes_other 0.004 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2798 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing