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Crystal structure of beta-xylosidase mutant (D281N, E517Q) from Thermotoga maritima in complex with xylopentaose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ZEQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.9 293 3% polyethylene glycol 8000, 48% 2-methyl-2,4-pentanediol, 0.1 M sodium cacodylate pH 5.9
Crystal Properties Matthews coefficient Solvent content 2.55 51.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.35 α = 90 b = 100.89 β = 90 c = 179.11 γ = 90
Symmetry Space Group P 21 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 175 PIXEL DECTRIS EIGER2 XE 16M 2022-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 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 1.52 50.445 99.9 0.097 0.114 0.06 0.999 9.6 6.9 272231
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 1.52 1.55 0.03 0.036 0.019 0.999 6.3
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 THROUGHOUT 1.52 50.445 272165 13593 99.807 0.166 0.1643 0.1643 0.1885 0.1884 20.402
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] 1.08 0.083 -1.163
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.391 r_dihedral_angle_3_deg 13.562 r_dihedral_angle_2_deg 7.781 r_dihedral_angle_1_deg 6.889 r_lrange_it 5.701 r_lrange_other 5.701 r_scangle_it 4.669 r_scangle_other 4.668 r_scbond_it 3.156 r_scbond_other 3.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.391 r_dihedral_angle_3_deg 13.562 r_dihedral_angle_2_deg 7.781 r_dihedral_angle_1_deg 6.889 r_lrange_it 5.701 r_lrange_other 5.701 r_scangle_it 4.669 r_scangle_other 4.668 r_scbond_it 3.156 r_scbond_other 3.156 r_mcangle_it 2.215 r_mcangle_other 2.215 r_mcbond_it 1.693 r_mcbond_other 1.691 r_angle_refined_deg 1.591 r_angle_other_deg 0.526 r_symmetry_nbd_refined 0.275 r_nbd_refined 0.217 r_nbd_other 0.197 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.14 r_symmetry_xyhbond_nbd_refined 0.127 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.08 r_ncsr_local_group_1 0.061 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11751 Nucleic Acid Atoms Solvent Atoms 1322 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing