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Glycogen phosphorylase complexed with 4-trifluoromethylbenzaldehyde-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 of protein in a buffer solution containing 10 mM BES pH 6.7, 1 mM EDTA, 3 mM DTT. Crystals were soaked with 10mM inhibitor in 20% DMSO for 7 hrs, pH 6.7, SMALL TUBES, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.49 50.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.915 α = 90 b = 128.915 β = 90 c = 116.965 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 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 2.07 99 93.1 0.081 10.47 4.7 56442 56442 -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) 2.07 2.11 77.8 0.473 2.81 3.2
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 2.07 56.43 53572 2860 93.19 0.19544 0.19339 0.1911 0.23505 0.2332 RANDOM 43.732
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] 0.17 0.17 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.246 r_dihedral_angle_4_deg 20.05 r_dihedral_angle_3_deg 16.218 r_dihedral_angle_1_deg 5.548 r_scangle_it 2.97 r_scbond_it 1.855 r_mcangle_it 1.314 r_angle_refined_deg 1.21 r_mcbond_it 0.768 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.246 r_dihedral_angle_4_deg 20.05 r_dihedral_angle_3_deg 16.218 r_dihedral_angle_1_deg 5.548 r_scangle_it 2.97 r_scbond_it 1.855 r_mcangle_it 1.314 r_angle_refined_deg 1.21 r_mcbond_it 0.768 r_nbtor_refined 0.309 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.166 r_symmetry_vdw_refined 0.162 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.089 r_bond_refined_d 0.01 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 193 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement CNS refinement HKL-3000 data collection DENZO data reduction SCALEPACK data scaling CNS phasing