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Crystal structure of beta-xylosidase mutant (E186Q/F503Y) from Bacillus pumilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZQJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 287 0.05 M HEPES (pH 7.5), 20% (w/v) PEG 3350, 1% (w/v) tryptone, and 30 mM xylobiose
Crystal Properties Matthews coefficient Solvent content 2.14 42.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.021 α = 90 b = 103.437 β = 123.08 c = 104.813 γ = 90
Symmetry Space Group C 1 2 1
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 315 2017-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.97940 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.78 50 96.1 0.085 0.094 0.038 13.86 4.7 95015
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.81 88.8 0.466 0.558 0.298 0.268 1.97 2.6
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 5ZQJ 1.782 35.633 1.53 83428 4243 83.8 0.168 0.1658 0.1656 0.2093 0.2089
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 4.116 f_angle_d 0.916 f_chiral_restr 0.059 f_bond_d 0.007 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8616 Nucleic Acid Atoms Solvent Atoms 555 Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement DENZO data reduction HKL-2000 data scaling MOLREP phasing