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Glycogen phosphorylase complexed with 4-methoxybenzaldehyde-4-(2,3,4,6-tetra-O-acetyl-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. 6.7mM inhibitor in 20% DMSO soaked with native crystals for 3 hrs, SMALL TUBES, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.45 49.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.31 α = 90 b = 128.31 β = 90 c = 116.05 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 1.95 35.58 97.8 0.07 18.3 5 69032 69032 -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) 1.95 2.06 97.2 0.366 5 4.9
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 2PRJ 1.95 31.11 65522 3490 97.36 0.18367 0.18197 0.1823 0.21606 0.2163 RANDOM 29.839
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 34.093 r_dihedral_angle_4_deg 19.727 r_dihedral_angle_3_deg 15.636 r_dihedral_angle_1_deg 5.472 r_scangle_it 3.113 r_scbond_it 1.826 r_mcangle_it 1.231 r_angle_refined_deg 1.15 r_mcbond_it 0.632 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.093 r_dihedral_angle_4_deg 19.727 r_dihedral_angle_3_deg 15.636 r_dihedral_angle_1_deg 5.472 r_scangle_it 3.113 r_scbond_it 1.826 r_mcangle_it 1.231 r_angle_refined_deg 1.15 r_mcbond_it 0.632 r_nbtor_refined 0.304 r_nbd_refined 0.181 r_symmetry_vdw_refined 0.144 r_symmetry_hbond_refined 0.104 r_xyhbond_nbd_refined 0.098 r_chiral_restr 0.086 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 6608 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement CNS refinement HKL-3000 data collection DENZO data reduction SCALEPACK data scaling CNS phasing