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Structure of the family43 beta-Xylosidase D128G mutant from geobacillus stearothermophilus in complex with xylobiose
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.4 285 17% PEG 6000, 0.1M MES, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 2.32 46.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.383 α = 90 b = 140.383 β = 90 c = 232.907 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 IMAGE PLATE MARRESEARCH 2005-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.9239 EMBL/DESY, HAMBURG X12
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.2 30 99.9 119520 118549
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.23 100
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.2 30 119250 118179 5922 99.68 0.208 0.208 0.205 0.2042 0.282 0.2805 RANDOM 36.489
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] -0.91 -0.91 1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.084 r_dihedral_angle_4_deg 19.32 r_dihedral_angle_3_deg 17.185 r_dihedral_angle_1_deg 7.256 r_scangle_it 2.539 r_scbond_it 1.717 r_angle_refined_deg 1.616 r_mcangle_it 1.257 r_mcbond_it 0.738 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.084 r_dihedral_angle_4_deg 19.32 r_dihedral_angle_3_deg 17.185 r_dihedral_angle_1_deg 7.256 r_scangle_it 2.539 r_scbond_it 1.717 r_angle_refined_deg 1.616 r_mcangle_it 1.257 r_mcbond_it 0.738 r_nbtor_refined 0.311 r_symmetry_hbond_refined 0.228 r_nbd_refined 0.216 r_symmetry_vdw_refined 0.215 r_metal_ion_refined 0.207 r_xyhbond_nbd_refined 0.201 r_chiral_restr 0.117 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17488 Nucleic Acid Atoms Solvent Atoms 1651 Heterogen Atoms 140
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction