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Glycogen phosphorylase complexed with 2-chlorobenzaldehyde-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 Crystals grown from 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 T-state native enzyme crystal for 11.5 hrs, SMALL TUBES, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.47 50.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.837 α = 90 b = 128.837 β = 90 c = 116.315 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 273 CCD MARMOSAIC 225 mm CCD 2008-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 0.979 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 30 99.5 0.077 12.35 4.7 71273 71273 -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 1.98 97.4 0.428 3.14 3
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 1.95 29.53 67586 67586 3611 99.49 0.18268 0.18099 0.1813 0.21477 0.2151 RANDOM 33.285
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] 0.02 0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.997 r_dihedral_angle_4_deg 18.097 r_dihedral_angle_3_deg 14.988 r_dihedral_angle_1_deg 5.333 r_scangle_it 3.192 r_scbond_it 1.851 r_mcangle_it 1.234 r_angle_refined_deg 1.155 r_mcbond_it 0.636 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.997 r_dihedral_angle_4_deg 18.097 r_dihedral_angle_3_deg 14.988 r_dihedral_angle_1_deg 5.333 r_scangle_it 3.192 r_scbond_it 1.851 r_mcangle_it 1.234 r_angle_refined_deg 1.155 r_mcbond_it 0.636 r_nbtor_refined 0.304 r_nbd_refined 0.183 r_symmetry_vdw_refined 0.139 r_xyhbond_nbd_refined 0.101 r_chiral_restr 0.086 r_symmetry_hbond_refined 0.061 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 6597 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement CNS refinement HKL-3000 data collection DENZO data reduction SCALEPACK data scaling CNS phasing