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Protein Structure of the First Glycoside Hydrolase Family 30, Subfamily 12 Endoxylanase
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 4.6 289 0.17 M ammonium acetate, 0.085 M sodium acetate HCl pH 4.6, 25.5 percent PEG 4000 and 15 percent glycerol
Crystal Properties Matthews coefficient Solvent content 2.86 56.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.307 α = 90 b = 133.392 β = 101.544 c = 137.7 γ = 90
Symmetry Space Group P 1 21 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 EIGER2 XE 9M 2024-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9857 NSLS-II 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.92 50.21 99.6 0.131 0.072 0.994 9.4 3.3 239756 32.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.92 1.95 96.2 1.157 0.649 0.403 0.89 2.9
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 THROUGHOUT 1.916 48.949 239538 11805 98.983 0.17 0.1686 0.1772 0.205 0.2116 RANDOM 25.988
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] 0.063 0.787 -0.577 0.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.504 r_dihedral_angle_3_deg 13.115 r_dihedral_angle_2_deg 7.418 r_dihedral_angle_1_deg 6.969 r_lrange_it 6.811 r_lrange_other 6.74 r_scangle_it 4.895 r_scangle_other 4.895 r_mcangle_it 3.651 r_mcangle_other 3.651
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.504 r_dihedral_angle_3_deg 13.115 r_dihedral_angle_2_deg 7.418 r_dihedral_angle_1_deg 6.969 r_lrange_it 6.811 r_lrange_other 6.74 r_scangle_it 4.895 r_scangle_other 4.895 r_mcangle_it 3.651 r_mcangle_other 3.651 r_scbond_it 3.14 r_scbond_other 3.14 r_mcbond_it 2.435 r_mcbond_other 2.434 r_angle_refined_deg 1.597 r_angle_other_deg 0.546 r_symmetry_xyhbond_nbd_refined 0.296 r_nbd_other 0.223 r_nbd_refined 0.217 r_symmetry_nbd_refined 0.211 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.17 r_metal_ion_refined 0.151 r_symmetry_xyhbond_nbd_other 0.123 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.076 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 19950 Nucleic Acid Atoms Solvent Atoms 1630 Heterogen Atoms 267
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing