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Crystal structure of glycogen phosphorylase complexed with an anthranilimide based inhibitor GSK055
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 6 290 12-25% MPD, 0.1M Na MES Buffer pH 6.0, 5mM Caffeine, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.84 56.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.368 α = 90 b = 124.368 β = 90 c = 123.621 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 1.9 50 99.9 0.078 21.58 5.8 168454 168259 -3 16.3
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 1.9 1.97 99.7 0.534 2.7 5.6 16870
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 1.9 38.63 168259 163245 5094 99.9 0.15436 0.15336 0.1619 0.18642 0.1937 RANDOM 19.612
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] -0.05 -0.03 -0.05 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.63 r_dihedral_angle_4_deg 17.475 r_dihedral_angle_3_deg 12.788 r_dihedral_angle_1_deg 5.732 r_scangle_it 2.794 r_scbond_it 1.837 r_angle_refined_deg 1.246 r_mcangle_it 1.195 r_angle_other_deg 0.921 r_mcbond_it 0.788
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.63 r_dihedral_angle_4_deg 17.475 r_dihedral_angle_3_deg 12.788 r_dihedral_angle_1_deg 5.732 r_scangle_it 2.794 r_scbond_it 1.837 r_angle_refined_deg 1.246 r_mcangle_it 1.195 r_angle_other_deg 0.921 r_mcbond_it 0.788 r_symmetry_vdw_other 0.263 r_symmetry_hbond_refined 0.25 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.205 r_nbd_other 0.189 r_nbtor_refined 0.18 r_mcbond_other 0.169 r_xyhbond_nbd_refined 0.126 r_nbtor_other 0.084 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_gen_planes_other 0.005 r_bond_other_d 0.002 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 13016 Nucleic Acid Atoms Solvent Atoms 1612 Heterogen Atoms 198
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing