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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 L-arabinose and 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 2.14 42.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.816 α = 90 b = 59.816 β = 90 c = 277.87 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 ADSC QUANTUM 210 2009-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.9334 ESRF ID14-1
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 1.695 41.937 99 0.072 0.077 0.028 17.7 7.5 57020
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 1.7 1.79 93.1 0.273 0.273 0.303 0.128 2.6 5.3
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 1.7 41.85 54015 2860 98.92 0.1608 0.1592 0.1591 0.1905 0.1907 RANDOM 16.832
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] 0.42 0.42 -0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.031 r_dihedral_angle_4_deg 14.848 r_dihedral_angle_3_deg 13.199 r_dihedral_angle_1_deg 6.789 r_angle_refined_deg 1.44 r_chiral_restr 0.102 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 516 Heterogen Atoms 41
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction COMBAT data reduction PHASER phasing