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Crystal structure of a thermostable glycoside hydrolase family 43 {beta}-1,4-xylosidase from Geobacillus thermoleovorans IT-08 in complex with D-xylose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YIF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 283 0.1M HEPES (N-(2-hydroxyethyl)piperazine-N-(2-ethanesulfonic acid)) buffer, pH 7.0, 5% (w/v) PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.33 47.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.453 α = 90 b = 62.453 β = 90 c = 276.672 γ = 90
Symmetry Space Group P 43 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 100 CCD MARMOSAIC 225 mm CCD 2009-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.9300 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.825 46.354 99.1 0.086 0.102 0.054 8.6 3.4 44217
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 96.7 0.297 0.297 0.361 0.199 1.7 3.1
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 (Observed) 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 1yif 1.9 46.35 40994 2186 96.82 0.2183 0.2161 0.2165 0.2591 0.2594 RANDOM 19.91
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] 0.19 0.19 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.493 r_dihedral_angle_4_deg 15.969 r_dihedral_angle_3_deg 13.909 r_dihedral_angle_1_deg 7.16 r_angle_refined_deg 1.448 r_chiral_restr 0.099 r_bond_refined_d 0.011 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4053 Nucleic Acid Atoms Solvent Atoms 531 Heterogen Atoms 11
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction COMBAT data reduction PHASER phasing