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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
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 2.17 43.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.989 α = 90 b = 59.989 β = 90 c = 278.987 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 4 2009-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.9330 ESRF ID14-2
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 2.1 45.481 99.9 0.122 0.132 0.049 12 6.9 31118
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 2.1 2.21 99.5 0.408 0.408 0.451 0.185 1.9 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1yif 2.1 45.48 29435 1574 99.89 0.1519 0.1493 0.1995 0.1864 RANDOM 18.955
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] 0.5 0.5 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.841 r_dihedral_angle_4_deg 14.15 r_dihedral_angle_3_deg 13.142 r_dihedral_angle_1_deg 7.341 r_angle_refined_deg 1.538 r_angle_other_deg 0.972 r_chiral_restr 0.097 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.841 r_dihedral_angle_4_deg 14.15 r_dihedral_angle_3_deg 13.142 r_dihedral_angle_1_deg 7.341 r_angle_refined_deg 1.538 r_angle_other_deg 0.972 r_chiral_restr 0.097 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4053 Nucleic Acid Atoms Solvent Atoms 471 Heterogen Atoms 11
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction COMBAT data reduction PHASER phasing