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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 Residues 24-203
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 1.98 38.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.911 α = 90 b = 89.103 β = 90 c = 47.135 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 PILATUS 6M 2020-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97626 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 1.128 47.14 98.74 0.995 6.13 2.2 221328
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 1.13 1.17 0.219
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 1.128 47.135 117455 5893 98.558 0.175 0.1735 0.1826 0.2007 0.2097 11.934
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] -1.256 -1.578 2.834
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.038 r_dihedral_angle_3_deg 13.27 r_dihedral_angle_1_deg 7.69 r_dihedral_angle_2_deg 7.286 r_rigid_bond_restr 5.639 r_lrange_it 2.37 r_lrange_other 2.267 r_scangle_it 1.69 r_scangle_other 1.689 r_angle_refined_deg 1.504
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.038 r_dihedral_angle_3_deg 13.27 r_dihedral_angle_1_deg 7.69 r_dihedral_angle_2_deg 7.286 r_rigid_bond_restr 5.639 r_lrange_it 2.37 r_lrange_other 2.267 r_scangle_it 1.69 r_scangle_other 1.689 r_angle_refined_deg 1.504 r_mcangle_it 1.471 r_mcangle_other 1.471 r_scbond_it 1.277 r_scbond_other 1.276 r_mcbond_it 1.105 r_mcbond_other 1.07 r_angle_other_deg 0.508 r_symmetry_nbd_refined 0.432 r_symmetry_xyhbond_nbd_refined 0.296 r_nbd_other 0.242 r_nbd_refined 0.22 r_symmetry_nbd_other 0.213 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.169 r_symmetry_nbtor_other 0.088 r_metal_ion_refined 0.086 r_chiral_restr 0.075 r_symmetry_metal_ion_refined 0.075 r_xyhbond_nbd_other 0.052 r_gen_planes_refined 0.012 r_bond_refined_d 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2798 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing