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Inactive Bacteroides ovatus GH98 endoxylanase E361A in complex with arabino-xylooligosaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other UNRELEASED SAD MODEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 Vapour diffusion
Crystal Properties Matthews coefficient Solvent content 2.3 46.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 186.05 α = 90 b = 63.485 β = 118.443 c = 180.9 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 2022-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.89842 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.8 53.02 99.9 0.22 0.259 0.136 0.982 6.2 6.9 46262
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.8 2.9 99.8 1.143 1.341 0.698 0.63 1.5 7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.8 53.02 46243 2395 99.829 0.19 0.1859 0.1851 0.268 0.2701 45.555
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] 0.547 -1.082 0.96 -0.212
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.968 r_dihedral_angle_6_deg 14.455 r_dihedral_angle_2_deg 10.227 r_dihedral_angle_1_deg 8.376 r_lrange_it 6.566 r_lrange_other 6.561 r_scangle_it 4.422 r_scangle_other 4.422 r_mcangle_it 4.34 r_mcangle_other 4.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.968 r_dihedral_angle_6_deg 14.455 r_dihedral_angle_2_deg 10.227 r_dihedral_angle_1_deg 8.376 r_lrange_it 6.566 r_lrange_other 6.561 r_scangle_it 4.422 r_scangle_other 4.422 r_mcangle_it 4.34 r_mcangle_other 4.34 r_scbond_it 2.751 r_scbond_other 2.751 r_mcbond_it 2.656 r_mcbond_other 2.656 r_angle_refined_deg 1.793 r_angle_other_deg 0.611 r_symmetry_xyhbond_nbd_refined 0.319 r_symmetry_nbd_refined 0.248 r_nbd_other 0.219 r_nbd_refined 0.209 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.158 r_metal_ion_refined 0.124 r_symmetry_xyhbond_nbd_other 0.123 r_ncsr_local_group_1 0.091 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.083 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14228 Nucleic Acid Atoms Solvent Atoms 317 Heterogen Atoms 157
Software Software Software Name Purpose REFMAC refinement PHASER phasing Coot model building DIALS data reduction DIALS data scaling