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Crystal structure of glycogen phosphorylase complexed with an anthranilimide based inhibitor GSK261
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EM6 PDB entry 1EM6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 12-25% MPD, 0.1M MES buffer pH 6.0, 5mm Caffeine, 30mM GlcNac, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.84 56.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.403 α = 90 b = 124.403 β = 90 c = 123.614 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 CCD ADSC QUANTUM 210 2005-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.00000 APS 17-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 1.8 50 96.8 0.087 11.5 3.2 197105 190798 -3 20.7
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 1.8 1.86 95.5 0.488 1.5 2.6 18805
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 (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 1EM6 1.8 19.66 190798 186135 5803 96.86 0.17468 0.17394 0.1829 0.19782 0.2054 RANDOM 25.015
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] -0.21 -0.1 -0.21 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.99 r_dihedral_angle_4_deg 14.066 r_dihedral_angle_3_deg 11.917 r_dihedral_angle_1_deg 5.469 r_scangle_it 1.967 r_scbond_it 1.295 r_angle_refined_deg 1.113 r_mcangle_it 0.903 r_angle_other_deg 0.842 r_mcbond_it 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.99 r_dihedral_angle_4_deg 14.066 r_dihedral_angle_3_deg 11.917 r_dihedral_angle_1_deg 5.469 r_scangle_it 1.967 r_scbond_it 1.295 r_angle_refined_deg 1.113 r_mcangle_it 0.903 r_angle_other_deg 0.842 r_mcbond_it 0.57 r_symmetry_vdw_other 0.254 r_nbd_refined 0.204 r_nbd_other 0.179 r_nbtor_refined 0.178 r_symmetry_vdw_refined 0.177 r_symmetry_hbond_refined 0.139 r_xyhbond_nbd_refined 0.117 r_mcbond_other 0.099 r_nbtor_other 0.081 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13003 Nucleic Acid Atoms Solvent Atoms 1353 Heterogen Atoms 224
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing