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Glycogen phosphorylase complexed with 4-chlorobenzaldehyde-4-(beta-D-glucopyranosyl)-thiosemicarbazone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 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 20mM inhibitor in 20% DMSO for 21 hrs, SMALL TUBES, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.44 49.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.15 α = 90 b = 128.15 β = 90 c = 115.97 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 2007-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 1.04498 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 35.69 97 0.054 21.3 5.4 63139 63139 -3 27.4
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 2.11 97.1 0.221 7.2 5.4 9172
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 2PRJ 2 35.69 59914 59914 3197 96.2 0.1945 0.19346 0.1938 0.21418 0.2183 RANDOM 31.102
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] 0.86 0.86 -1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.759 r_dihedral_angle_4_deg 18.259 r_dihedral_angle_3_deg 15.411 r_dihedral_angle_1_deg 5.149 r_scangle_it 2.04 r_scbond_it 1.256 r_angle_refined_deg 1.026 r_mcangle_it 0.966 r_mcbond_it 0.562 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.759 r_dihedral_angle_4_deg 18.259 r_dihedral_angle_3_deg 15.411 r_dihedral_angle_1_deg 5.149 r_scangle_it 2.04 r_scbond_it 1.256 r_angle_refined_deg 1.026 r_mcangle_it 0.966 r_mcbond_it 0.562 r_nbtor_refined 0.304 r_nbd_refined 0.183 r_symmetry_vdw_refined 0.138 r_xyhbond_nbd_refined 0.101 r_symmetry_hbond_refined 0.101 r_chiral_restr 0.074 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6604 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement CNS refinement HKL-3000 data collection DENZO data reduction SCALEPACK data scaling CNS phasing