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Glucopyranosylidene-spiro-iminothiazolidinone, a New Bicyclic Ring System: Synthesis, Derivatization, and Evaluation as Glycogen Phosphorylase Inhibitors by Enzyme Kinetic and Crystallographic Methods
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PYD PDB ENTRY 2PYD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.8 25MG/ML ENZYME, 1MM SPERMINE, 10MM BES, 3MM DTT, 0.1MM EDTA, 0.02% SODIUM AZIDE, PH 6.7
Crystal Properties Matthews coefficient Solvent content 2.46 49.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.24 α = 90 b = 128.24 β = 90 c = 115.9 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 MARRESEARCH MIRRORS 2007-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 SRS PX10.1
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 1.95 35.7 98 0.06 20.4 5.3 69137 25.4
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 1.95 2.06 96.8 0.38 5.1 5.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2PYD 1.95 35.71 65603 3502 97.69 0.17392 0.17274 0.179 0.19574 0.1972 RANDOM 31.349
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 r_dihedral_angle_2_deg 33.833 r_dihedral_angle_4_deg 17.235 r_dihedral_angle_3_deg 13.74 r_dihedral_angle_1_deg 5.268 r_mcangle_it 2.026 r_scbond_it 1.466 r_mcbond_it 1.197 r_mcbond_other 1.196 r_angle_refined_deg 1.039 r_angle_other_deg 0.719
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.833 r_dihedral_angle_4_deg 17.235 r_dihedral_angle_3_deg 13.74 r_dihedral_angle_1_deg 5.268 r_mcangle_it 2.026 r_scbond_it 1.466 r_mcbond_it 1.197 r_mcbond_other 1.196 r_angle_refined_deg 1.039 r_angle_other_deg 0.719 r_chiral_restr 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6562 Nucleic Acid Atoms Solvent Atoms 274 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing