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Crystal structure of beta-xylosidase from Thermotoga maritima in complex with xylohexaose hydrolysed to xylobiose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ZEQ D_1292121589
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 2.54 51.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.53 α = 90 b = 98.72 β = 90 c = 100.7 γ = 90
Symmetry Space Group P 21 21 2
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 2021-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.51 87.71 100 1 56.5 13.4 259769
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.51 1.54 0.323
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT D_1292121589 1.51 87.709 259668 12762 93.495 0.168 0.1671 0.1671 0.19 0.1901 23.351
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] -1.224 2.552 -1.328
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.306 r_dihedral_angle_4_deg 17.876 r_dihedral_angle_3_deg 12.53 r_dihedral_angle_1_deg 7.016 r_lrange_it 5.083 r_lrange_other 5.016 r_scangle_it 4.441 r_scangle_other 4.441 r_scbond_it 3.03 r_scbond_other 3.029
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.306 r_dihedral_angle_4_deg 17.876 r_dihedral_angle_3_deg 12.53 r_dihedral_angle_1_deg 7.016 r_lrange_it 5.083 r_lrange_other 5.016 r_scangle_it 4.441 r_scangle_other 4.441 r_scbond_it 3.03 r_scbond_other 3.029 r_mcangle_it 2.2 r_mcangle_other 2.2 r_angle_refined_deg 1.673 r_mcbond_it 1.667 r_mcbond_other 1.667 r_angle_other_deg 1.472 r_nbd_refined 0.211 r_symmetry_nbd_other 0.177 r_nbtor_refined 0.169 r_nbd_other 0.139 r_symmetry_nbd_refined 0.138 r_xyhbond_nbd_refined 0.116 r_symmetry_xyhbond_nbd_refined 0.105 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.08 r_ncsr_local_group_1 0.052 r_symmetry_xyhbond_nbd_other 0.04 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11867 Nucleic Acid Atoms Solvent Atoms 1023 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing