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Glycogen phosphorylase complexed with 4-pyridinecarboxaldehyde-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 20 mg/ml of protein in a buffer solution containing 10 mM BES pH 6.7, 1 mM EDTA and 3 mM DTT. 20mM inhibitor in 20% DMSO soaked with crystal for 7 hrs, SMALL TUBES, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.45 49.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.501 α = 90 b = 128.501 β = 90 c = 115.955 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 ADSC QUANTUM 4 2007-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8081 EMBL/DESY, HAMBURG X13
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 1.98 30 99 0.057 20.15 6.1 66434 66434 -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) 1.98 2.03 97.7 0.472 5.13 6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 2PRJ 1.98 29.44 62917 62914 3372 97.7 0.18292 0.18118 0.21552 0.2147 RANDOM 27.616
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 0.05 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.228 r_dihedral_angle_4_deg 20.089 r_dihedral_angle_3_deg 16.011 r_dihedral_angle_1_deg 5.444 r_scangle_it 3.11 r_scbond_it 1.827 r_mcangle_it 1.205 r_angle_refined_deg 1.156 r_mcbond_it 0.615 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.228 r_dihedral_angle_4_deg 20.089 r_dihedral_angle_3_deg 16.011 r_dihedral_angle_1_deg 5.444 r_scangle_it 3.11 r_scbond_it 1.827 r_mcangle_it 1.205 r_angle_refined_deg 1.156 r_mcbond_it 0.615 r_nbtor_refined 0.303 r_nbd_refined 0.182 r_symmetry_hbond_refined 0.147 r_symmetry_vdw_refined 0.144 r_xyhbond_nbd_refined 0.1 r_chiral_restr 0.087 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 224 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement CNS refinement HKL-3000 data collection DENZO data reduction SCALEPACK data scaling CNS phasing