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Crystal structure of beta-xylosidase from Thermotoga maritima in complex with methyl-beta-D-xylopyranoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JP0 5JP0, 5Z9S, 5YOT, 3U4A, 5XXL experimental model PDB 5Z9S 5JP0, 5Z9S, 5YOT, 3U4A, 5XXL experimental model PDB 5YOT 5JP0, 5Z9S, 5YOT, 3U4A, 5XXL experimental model PDB 3U4A 5JP0, 5Z9S, 5YOT, 3U4A, 5XXL experimental model PDB 5XXL 5JP0, 5Z9S, 5YOT, 3U4A, 5XXL
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 2.52 51.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.62 α = 90 b = 97.68 β = 90 c = 100.69 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 2020-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 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 1.46 51.25 100 1 64.2 13.1 302573
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 1.46 1.49 0.331
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 5JP0, 5Z9S, 5YOT, 3U4A, 5XXL 1.46 51.25 302502 15107 99.549 0.173 0.1717 0.1717 0.1909 0.1909 28.782
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] -1.78 2.139 -0.359
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.709 r_dihedral_angle_4_deg 18.142 r_dihedral_angle_3_deg 12.989 r_dihedral_angle_1_deg 6.588 r_lrange_it 5.487 r_scangle_it 5.262 r_scbond_it 3.782 r_mcangle_it 2.657 r_mcbond_it 2.068 r_angle_refined_deg 1.743
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.709 r_dihedral_angle_4_deg 18.142 r_dihedral_angle_3_deg 12.989 r_dihedral_angle_1_deg 6.588 r_lrange_it 5.487 r_scangle_it 5.262 r_scbond_it 3.782 r_mcangle_it 2.657 r_mcbond_it 2.068 r_angle_refined_deg 1.743 r_nbtor_refined 0.319 r_nbd_refined 0.203 r_symmetry_nbd_refined 0.162 r_symmetry_xyhbond_nbd_refined 0.142 r_chiral_restr 0.12 r_xyhbond_nbd_refined 0.1 r_ncsr_local_group_1 0.059 r_bond_refined_d 0.011 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11856 Nucleic Acid Atoms Solvent Atoms 813 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing