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Crystal structure of exo-glucosidase/glucosaminidase VC0615 from Vibrio Cholerae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H7L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 100 mM Tris pH 7.5, 5% PGA-LM, 8% PEG 20k
Crystal Properties Matthews coefficient Solvent content 3.16 61.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 234.899 α = 90 b = 234.899 β = 90 c = 129.421 γ = 120
Symmetry Space Group P 32 2 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 PILATUS3 6M 2017-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim 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 3.17 47.33 100 0.08 0.997 8.4 11.5 69816 74
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.17 3.24 100 0.904 0.322 0.9 10.8
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 THROUGHOUT 3H7L 3.17 47.33 66351 3411 99.85 0.23742 0.23534 0.2379 0.27978 0.2852 RANDOM 103.012
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] -0.3 -0.15 -0.3 0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.914 r_dihedral_angle_4_deg 19.166 r_dihedral_angle_3_deg 16.951 r_long_range_B_refined 15.539 r_long_range_B_other 15.539 r_mcangle_it 12.192 r_mcangle_other 12.192 r_scangle_other 11.859 r_mcbond_it 7.953 r_mcbond_other 7.946
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.914 r_dihedral_angle_4_deg 19.166 r_dihedral_angle_3_deg 16.951 r_long_range_B_refined 15.539 r_long_range_B_other 15.539 r_mcangle_it 12.192 r_mcangle_other 12.192 r_scangle_other 11.859 r_mcbond_it 7.953 r_mcbond_other 7.946 r_scbond_it 7.616 r_scbond_other 7.616 r_dihedral_angle_1_deg 7.201 r_angle_refined_deg 1.128 r_angle_other_deg 0.859 r_chiral_restr 0.055 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 22634 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing