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Glycoside hydrolase family 16 endo-glucanase from Bacteroides ovatus in complex with G4G4G3G-NHCOCH2Br
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 293 0.1 M succinic acid pH 7.2,
15 % (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.07 40.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.58 α = 90 b = 61.15 β = 93.608 c = 49.411 γ = 90
Symmetry Space Group C 1 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 EIGER X 16M 2019-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
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 2.148 84.123 96 0.993 7 1.8 27458
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 2.3 2.44 0.76
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 2.148 84.123 27458 1311 99.507 0.187 0.1857 0.1857 0.2067 0.2066 28.927
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] 1.798 1.226 -0.576 -1.365
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.626 r_dihedral_angle_3_deg 13.921 r_dihedral_angle_4_deg 9.73 r_dihedral_angle_1_deg 8.497 r_lrange_it 4.295 r_lrange_other 4.269 r_scangle_it 3.273 r_scangle_other 3.267 r_angle_other_deg 2.482 r_mcangle_other 2.361
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.626 r_dihedral_angle_3_deg 13.921 r_dihedral_angle_4_deg 9.73 r_dihedral_angle_1_deg 8.497 r_lrange_it 4.295 r_lrange_other 4.269 r_scangle_it 3.273 r_scangle_other 3.267 r_angle_other_deg 2.482 r_mcangle_other 2.361 r_mcangle_it 2.36 r_scbond_it 2.043 r_scbond_other 2.037 r_mcbond_it 1.543 r_mcbond_other 1.538 r_angle_refined_deg 1.388 r_symmetry_nbd_other 0.206 r_nbd_refined 0.183 r_nbtor_refined 0.163 r_nbd_other 0.15 r_xyhbond_nbd_refined 0.148 r_symmetry_xyhbond_nbd_refined 0.101 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.056 r_symmetry_nbd_refined 0.047 r_bond_other_d 0.036 r_gen_planes_other 0.007 r_bond_refined_d 0.006 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3770 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction Coot model building PHASER phasing XSCALE data scaling