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Synthesis of C-D-Glycopyranosyl-Hydroquinones and-Benzoquinones. Inhibition of PTP1B. Inhibition of and binding to glycogen phosphorylase in the crystal
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PRJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SMALL TUBES 6.7 289 10 mM Bes buffer, 3 mM DDT, pH 6.7, SMALL TUBES, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.44 49.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.173 α = 90 b = 128.173 β = 90 c = 115.795 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 298 CCD ADSC QUANTUM 4 2003-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.803 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.03 21.36 97.7 0.059 13.4 4.4 61307 61307 -3 32.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.03 2.06 98.2 0.532 4.1 4.4 3029
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 2PRJ 2.03 21.36 61276 61276 3091 97.7 0.188 0.188 0.187 0.212 RANDOM 39.1
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] 4.39 4.39 -8.78
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.6 c_scangle_it 3.33 c_scbond_it 2.19 c_mcangle_it 2.04 c_mcbond_it 1.31 c_angle_deg 1.2 c_improper_angle_d 0.77 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6558 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 34
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement CNS phasing