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Bacteroides ovatus GH98 endoxylanase in complex with arabino-xylooligosaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other From unreleased SAD data
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 Vapour diffusion
Crystal Properties Matthews coefficient Solvent content 2.3 46.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 186.05 α = 90 b = 63.85 β = 118.69 c = 180.49 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 PILATUS 6M 2022-01-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.93932 Diamond I04
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 2.2 59.18 99.9 0.995 9.3 1.9 94781
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 2.2 2.24 100 0.643 1.4 2
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.2 59.176 94779 4758 99.924 0.195 0.1922 0.2454 0.2425 40.87
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] 1.257 -1.005 0.671 -0.518
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.574 r_dihedral_angle_3_deg 13.351 r_dihedral_angle_2_deg 10.501 r_dihedral_angle_1_deg 8.007 r_lrange_it 5.334 r_lrange_other 5.319 r_scangle_it 3.397 r_scangle_other 3.397 r_mcangle_it 3.301 r_mcangle_other 3.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.574 r_dihedral_angle_3_deg 13.351 r_dihedral_angle_2_deg 10.501 r_dihedral_angle_1_deg 8.007 r_lrange_it 5.334 r_lrange_other 5.319 r_scangle_it 3.397 r_scangle_other 3.397 r_mcangle_it 3.301 r_mcangle_other 3.3 r_scbond_it 2.127 r_scbond_other 2.127 r_mcbond_it 2.015 r_mcbond_other 2.014 r_angle_refined_deg 1.635 r_angle_other_deg 0.56 r_symmetry_nbd_refined 0.248 r_nbd_refined 0.209 r_symmetry_nbd_other 0.192 r_nbd_other 0.19 r_nbtor_refined 0.185 r_symmetry_xyhbond_nbd_refined 0.175 r_xyhbond_nbd_refined 0.162 r_metal_ion_refined 0.134 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.077 r_ncsr_local_group_1 0.076 r_symmetry_xyhbond_nbd_other 0.047 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14243 Nucleic Acid Atoms Solvent Atoms 534 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data reduction Coot model building Aimless data scaling PHASER phasing