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D-GlcNAc-bound structure of Vibrio vulnificus putative carbohydrate binding module and split domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6X7T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295.15 0.2 M Sodium acetate, 0.1 M Bis-tris propane pH 7.5, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.49 64.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.58 α = 90 b = 189.49 β = 90 c = 199.69 γ = 90
Symmetry Space Group I 2 2 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 EIGER X 9M 2026-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.95371 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.28 50 100 0.115 0.12 0.998 12.94 13.7 103968
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.28 2.34 3.216 3.348 0.353
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 2.28 48.81 98698 5270 99.96 0.1934 0.1918 0.1959 0.22267 0.2237 RANDOM 77.018
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] -0.46 1.16 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.257 r_dihedral_angle_2_deg 13.246 r_long_range_B_other 11.492 r_long_range_B_refined 11.491 r_scangle_other 9.377 r_dihedral_angle_1_deg 9.245 r_mcangle_other 8.165 r_mcangle_it 8.164 r_scbond_other 7.625 r_scbond_it 7.623
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.257 r_dihedral_angle_2_deg 13.246 r_long_range_B_other 11.492 r_long_range_B_refined 11.491 r_scangle_other 9.377 r_dihedral_angle_1_deg 9.245 r_mcangle_other 8.165 r_mcangle_it 8.164 r_scbond_other 7.625 r_scbond_it 7.623 r_mcbond_it 6.429 r_mcbond_other 6.424 r_angle_refined_deg 2.381 r_angle_other_deg 0.887 r_chiral_restr 0.143 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10742 Nucleic Acid Atoms Solvent Atoms 305 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction PDB_EXTRACT data extraction MOLREP phasing