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GH10 family xylanase XynA from Bacillus sp. KW1 complex with xylobiosyl-configured cyclophellitol probe bearing an alpha-1,3 - Araf decoration
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 20% PEG3350, 0.2M KSCN
Crystal Properties Matthews coefficient Solvent content 2.53 51.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.065 α = 90 b = 109.065 β = 90 c = 84.791 γ = 90
Symmetry Space Group P 41 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 EIGER2 XE 16M 2024-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 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 2.02 57.05 100 0.11 0.116 0.037 0.999 14.2 17.8 34175
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) 2.02 2.07 99.6 3.949 4.177 1.354 0.309 0.7 18.1
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.02 54.592 34111 1705 99.962 0.203 0.2014 0.2071 0.2345 0.2433 RANDOM 65.249
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] 0.605 0.605 -1.211
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.204 r_dihedral_angle_3_deg 12.561 r_dihedral_angle_2_deg 10.025 r_dihedral_angle_1_deg 8.629 r_lrange_it 6.736 r_lrange_other 6.736 r_scangle_it 5.476 r_scangle_other 5.475 r_scbond_it 3.787 r_scbond_other 3.787
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.204 r_dihedral_angle_3_deg 12.561 r_dihedral_angle_2_deg 10.025 r_dihedral_angle_1_deg 8.629 r_lrange_it 6.736 r_lrange_other 6.736 r_scangle_it 5.476 r_scangle_other 5.475 r_scbond_it 3.787 r_scbond_other 3.787 r_mcangle_it 3.71 r_mcangle_other 3.71 r_mcbond_it 2.709 r_mcbond_other 2.707 r_angle_refined_deg 1.948 r_angle_other_deg 0.967 r_nbd_refined 0.161 r_nbtor_refined 0.153 r_symmetry_nbd_other 0.126 r_xyhbond_nbd_refined 0.12 r_chiral_restr 0.107 r_nbd_other 0.089 r_symmetry_nbd_refined 0.076 r_symmetry_xyhbond_nbd_refined 0.074 r_symmetry_nbtor_other 0.065 r_gen_planes_refined 0.01 r_bond_refined_d 0.009 r_gen_planes_other 0.005 r_bond_other_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3104 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 27
Software Software Software Name Purpose DIALS data reduction Aimless data scaling REFMAC refinement MOLREP phasing