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Crystal structure of Aspergillus niger GH11 endoxylanase XynA in complex with xylobiose epoxide activity based probe
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QZ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M MES pH 5.5, 0.1 M NaCl, 1.8 M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.41 48.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.508 α = 90 b = 67.508 β = 90 c = 165.752 γ = 120
Symmetry Space Group P 65 2 2
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 6M 2018-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976220 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.79 47.77 100 0.033 12.8 23.3 21974
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.79 1.83 100 0.743 1.2 23.6
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2qz2 1.79 47.77 20827 1082 99.95 0.17901 0.17673 0.1884 0.22259 0.2386 RANDOM 31.718
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] 1.02 0.51 1.02 -3.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.114 r_dihedral_angle_4_deg 14.362 r_dihedral_angle_3_deg 10.562 r_dihedral_angle_1_deg 8.943 r_long_range_B_refined 6.701 r_long_range_B_other 6.699 r_scangle_other 5.679 r_scbond_it 4.021 r_scbond_other 4.019 r_mcangle_it 3.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.114 r_dihedral_angle_4_deg 14.362 r_dihedral_angle_3_deg 10.562 r_dihedral_angle_1_deg 8.943 r_long_range_B_refined 6.701 r_long_range_B_other 6.699 r_scangle_other 5.679 r_scbond_it 4.021 r_scbond_other 4.019 r_mcangle_it 3.3 r_mcangle_other 3.3 r_mcbond_it 2.634 r_mcbond_other 2.63 r_angle_refined_deg 1.658 r_angle_other_deg 1.566 r_chiral_restr 0.073 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1401 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling REFMAC phasing