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Crystal structure of glycogen phophorylase complexed with an anthranilimide based inhibitor GSK254
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 0.1M Na MES pH 5.8-6.1, 12-25% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.81 56.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.103 α = 90 b = 124.103 β = 90 c = 123.222 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) 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 2.4 50 99.2 0.106 0.106 14.9 5.5 83085 82440 25.8
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 1EM6 2.57 49.27 65493 2049 99.95 0.16865 0.16744 0.1713 0.20729 0.2096 RANDOM 37.29
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] -0.61 -0.31 -0.61 0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.773 r_dihedral_angle_4_deg 15.157 r_dihedral_angle_3_deg 13.04 r_dihedral_angle_1_deg 5.542 r_scangle_it 1.145 r_angle_refined_deg 1.055 r_angle_other_deg 0.81 r_scbond_it 0.749 r_mcangle_it 0.715 r_mcbond_it 0.437
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.773 r_dihedral_angle_4_deg 15.157 r_dihedral_angle_3_deg 13.04 r_dihedral_angle_1_deg 5.542 r_scangle_it 1.145 r_angle_refined_deg 1.055 r_angle_other_deg 0.81 r_scbond_it 0.749 r_mcangle_it 0.715 r_mcbond_it 0.437 r_symmetry_hbond_refined 0.289 r_symmetry_vdw_refined 0.241 r_nbd_refined 0.194 r_symmetry_vdw_other 0.186 r_nbtor_refined 0.179 r_nbd_other 0.175 r_xyhbond_nbd_refined 0.121 r_nbtor_other 0.081 r_mcbond_other 0.062 r_chiral_restr 0.054 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.002 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 13062 Nucleic Acid Atoms Solvent Atoms 540 Heterogen Atoms 226
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing