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Glucuronoxylan-specific GH30_8 family xylanase CtXyn30A from Clostridium thermocellum complex with glucuronic acid epoxide inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CKQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 292 100 mM Tris-HCl pH 8.5, 12% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.59 52.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.071 α = 98.395 b = 60.514 β = 97.404 c = 83.88 γ = 105.501
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 EIGER2 XE 16M 2023-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 1.5 48.44 98 0.071 0.1 0.071 0.991 7.4 3.6 147933
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) 1.5 1.53 96.7 0.646 0.913 0.646 0.631 1.3 3.7
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 1.5 48.44 147844 7296 97.935 0.19 0.189 0.1986 0.2147 0.2241 15.224
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] 0.176 -0.047 0.729 0.113 -0.184 -0.403
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.654 r_dihedral_angle_3_deg 10.808 r_dihedral_angle_2_deg 9.333 r_dihedral_angle_1_deg 7.282 r_lrange_it 4.049 r_lrange_other 3.815 r_scangle_it 2.849 r_scangle_other 2.849 r_scbond_it 1.954 r_scbond_other 1.954
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.654 r_dihedral_angle_3_deg 10.808 r_dihedral_angle_2_deg 9.333 r_dihedral_angle_1_deg 7.282 r_lrange_it 4.049 r_lrange_other 3.815 r_scangle_it 2.849 r_scangle_other 2.849 r_scbond_it 1.954 r_scbond_other 1.954 r_angle_refined_deg 1.95 r_mcangle_it 1.835 r_mcangle_other 1.834 r_mcbond_it 1.346 r_mcbond_other 1.344 r_angle_other_deg 0.995 r_chiral_restr 0.238 r_nbd_refined 0.195 r_nbtor_refined 0.162 r_nbd_other 0.155 r_symmetry_nbd_other 0.143 r_xyhbond_nbd_refined 0.108 r_symmetry_nbd_refined 0.107 r_symmetry_xyhbond_nbd_refined 0.098 r_symmetry_nbtor_other 0.064 r_ncsr_local_group_1 0.054 r_bond_refined_d 0.012 r_bond_other_d 0.005 r_gen_planes_refined 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6252 Nucleic Acid Atoms Solvent Atoms 897 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling DIALS data reduction gemmi data extraction MOLREP phasing