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The crystal structure of 6-P-beta-D-Glucosidase (E375Q mutant) from Streptococcus mutans UA150 in complex with Gentiobiose 6-phosphate.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PN8 PDB entry 3PN8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 0.2M NaCl, 0.1M Bis-Tris:HCl,
25% (w/v) PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.22 44.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.22 α = 90 b = 91.796 β = 102.23 c = 94.225 γ = 90
Symmetry Space Group P 1 21 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 Mirror 2012-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97931 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.291 46 99.1 0.122 13.7 3.4 43091 43091
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 96.4 0.652 1.7 3.2
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 PDB entry 3PN8 2.291 46 1.34 43064 43064 2162 98.57 0.18 0.1768 0.1747 0.2389 0.2359
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] 1.4886 11.9838 -9.2527 7.764
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.414 f_angle_d 1.016 f_chiral_restr 0.068 f_bond_d 0.008 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7791 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 68
Software Software Software Name Purpose SBC-Collect data collection MOLREP phasing PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling