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Glycogen phosphorylase complexed with 3-bromobenzaldehyde-4-(beta-D-glucopyranosyl)-thiosemicarbazone
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 Crystals grown from 20 mg/ml protein in a buffer of 10 mM BES, pH 6.7, 1mM EDTA, 3mM DTT. Crystals soaked with 10mM inhibitor in 20% DMSO soaked for 21 hrs, SMALL TUBES, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.49 50.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.916 α = 90 b = 128.916 β = 90 c = 116.782 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 293 CCD MARMOSAIC 225 mm CCD 2008-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 0.97976 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 2.23 30 98.1 0.071 9.67 3.6 47672 47672 -3 36.5
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) 2.23 2.27 96.6 0.462 3.55 3.7 2290
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 2.23 30 45222 45222 2413 98.19 0.19763 0.19575 0.1956 0.23282 0.2326 RANDOM 42.343
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] 0.08 0.08 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.701 r_dihedral_angle_4_deg 19.58 r_dihedral_angle_3_deg 16.03 r_dihedral_angle_1_deg 5.264 r_scangle_it 2.204 r_scbond_it 1.371 r_angle_refined_deg 1.099 r_mcangle_it 1.08 r_mcbond_it 0.619 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.701 r_dihedral_angle_4_deg 19.58 r_dihedral_angle_3_deg 16.03 r_dihedral_angle_1_deg 5.264 r_scangle_it 2.204 r_scbond_it 1.371 r_angle_refined_deg 1.099 r_mcangle_it 1.08 r_mcbond_it 0.619 r_nbtor_refined 0.305 r_nbd_refined 0.189 r_symmetry_vdw_refined 0.18 r_symmetry_hbond_refined 0.154 r_xyhbond_nbd_refined 0.118 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6604 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement CNS refinement HKL-3000 data collection DENZO data reduction SCALEPACK data scaling CNS phasing