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Glycogen phosphorylase complexed with 2,5-dihydroxy-4-(beta-D-glucopyranosyl)-bromo-benzene
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PRJ PDB ENTRY 2PRJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SMALL TUBES 6.7 289 20 mg/mL protein in a buffer consisting of 10 mM BES, 0.5 mM EDTA, 3 mM DTT. T-state GPb crystals soaked with 20 mM inhibitor for 6 hrs, pH 6.7, SMALL TUBES, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.47 50.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.702 α = 90 b = 128.702 β = 90 c = 116.439 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 MARMOSAIC 225 mm CCD 2005-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 1.488 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 1.969 30 93.9 0.065 11.3 3.7 64845 64845 -3 26.5
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 1.969 2 90 0.298 4.2 3.8 3109
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 2PRJ 1.969 30 61530 61530 3267 93.2 0.19194 0.19082 0.1904 0.21271 0.2114 RANDOM 27.836
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] 0.76 0.76 -1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.647 r_dihedral_angle_4_deg 19.753 r_dihedral_angle_3_deg 14.864 r_dihedral_angle_1_deg 5.03 r_scangle_it 1.905 r_scbond_it 1.202 r_angle_refined_deg 1.022 r_mcangle_it 0.888 r_mcbond_it 0.521 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.647 r_dihedral_angle_4_deg 19.753 r_dihedral_angle_3_deg 14.864 r_dihedral_angle_1_deg 5.03 r_scangle_it 1.905 r_scbond_it 1.202 r_angle_refined_deg 1.022 r_mcangle_it 0.888 r_mcbond_it 0.521 r_nbtor_refined 0.302 r_nbd_refined 0.181 r_symmetry_vdw_refined 0.143 r_xyhbond_nbd_refined 0.093 r_chiral_restr 0.074 r_symmetry_hbond_refined 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6604 Nucleic Acid Atoms Solvent Atoms 335 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement CNS refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling CNS phasing