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Crystal structure of apo-alpha glucosidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F0E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 0.09 M NPS, 0.1 M Buffer System 1 (pH 7.0), 29% (v/v) P500MME P20K
Crystal Properties Matthews coefficient Solvent content 3.45 64.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.966 α = 90 b = 102.966 β = 90 c = 240.596 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M Adjustable focus K-B pair Si plus Pt, Rh coatings 2019-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.997 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.29 47.33 99.85 0.125 0.967 8.246 2.8 128793 44.16
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.29 2.37 99.73 0.649 2.7
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 THROUGHOUT 5F0E 2.29 47.33 1.98 128793 2019 99.84 0.18 0.1796 0.1819 0.2063 0.2065 49.8476
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14872 Nucleic Acid Atoms Solvent Atoms 680 Heterogen Atoms 145
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing