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Crystal structure of substrate bound GH5_22 exo-beta-xylosidase from the seaweed-derived thermophile Geobacillus thermodenitrificans OS27
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CEO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1 M MES-NaOH, 26% PEG 6000
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.479 α = 90 b = 92.01 β = 90 c = 106.326 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 9M 2019-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 0.9999 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 46.03 99.5 0.151 0.061 0.992 7.5 7.1 255519 13.57
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.52 1.55 96 0.917 0.372 0.702 1.9 6.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1CEO 1.52 46.03 0.01 255519 13027 98.68 0.1629 0.1613 0.1579 0.1944 0.1911 19.02
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.2409 f_angle_d 1.0591 f_chiral_restr 0.0561 f_plane_restr 0.0092 f_bond_d 0.0089
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7851 Nucleic Acid Atoms Solvent Atoms 944 Heterogen Atoms 46
Software Software Software Name Purpose PHENIX refinement Coot model building Aimless data scaling MoRDa phasing XDS data reduction