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Glycoside hydrolase family 16 endo-glucanase from Bacteroides ovatus in complex with G4G3G-2F-DNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NBO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 278 0.2 M sodium chloride,
0.1 M Tris pH 8.5,
25% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.15 42.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.447 α = 90 b = 84.576 β = 93.983 c = 67.105 γ = 90
Symmetry Space Group P 1 21 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 S 6M 2020-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.979 SSRL BL12-2
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 1.56 39.4 98.7 1 14.2 2 143215
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 1.56 1.59 0.935
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5NBO 1.56 39.4 72529 3598 98.568 0.173 0.1722 0.1723 0.1985 0.1986 24.81
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] 0.829 -2.23 0.966 -1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.116 r_dihedral_angle_4_deg 17.786 r_dihedral_angle_3_deg 12.465 r_dihedral_angle_1_deg 8.235 r_lrange_it 5.332 r_lrange_other 5.265 r_scangle_it 4.46 r_scangle_other 4.46 r_scbond_it 2.991 r_scbond_other 2.991
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.116 r_dihedral_angle_4_deg 17.786 r_dihedral_angle_3_deg 12.465 r_dihedral_angle_1_deg 8.235 r_lrange_it 5.332 r_lrange_other 5.265 r_scangle_it 4.46 r_scangle_other 4.46 r_scbond_it 2.991 r_scbond_other 2.991 r_mcangle_other 2.926 r_mcangle_it 2.919 r_angle_other_deg 2.704 r_mcbond_it 2.177 r_mcbond_other 2.161 r_angle_refined_deg 1.707 r_symmetry_nbd_other 0.213 r_nbd_refined 0.183 r_nbtor_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.16 r_xyhbond_nbd_refined 0.15 r_symmetry_nbd_refined 0.116 r_nbd_other 0.116 r_symmetry_nbtor_other 0.092 r_chiral_restr 0.082 r_bond_other_d 0.036 r_gen_planes_other 0.018 r_bond_refined_d 0.012 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3737 Nucleic Acid Atoms Solvent Atoms 374 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement XDS data reduction Coot model building PHASER phasing