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Glycogen phosphorylase complexed with 3-hydroxybenzaldehyde-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 20mM inhibitor in 20% DMSO soaked with T-state native enzyme crystals for 3.5 hrs, pH 6.7, SMALL TUBES, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.48 50.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.866 α = 90 b = 128.866 β = 90 c = 116.324 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 1.94 30 99.4 0.087 9.73 5.2 72392 72392 -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) 1.94 1.97 100 0.529 3.7 5.2
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 1.94 29.09 68578 68577 3643 99.24 0.1935 0.19226 0.1925 0.21633 0.2169 RANDOM 34.636
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] 0.07 0.07 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.708 r_dihedral_angle_4_deg 20.055 r_dihedral_angle_3_deg 15.436 r_dihedral_angle_1_deg 5.421 r_scangle_it 3.279 r_scbond_it 1.928 r_mcangle_it 1.277 r_angle_refined_deg 1.189 r_mcbond_it 0.659 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.708 r_dihedral_angle_4_deg 20.055 r_dihedral_angle_3_deg 15.436 r_dihedral_angle_1_deg 5.421 r_scangle_it 3.279 r_scbond_it 1.928 r_mcangle_it 1.277 r_angle_refined_deg 1.189 r_mcbond_it 0.659 r_nbtor_refined 0.304 r_nbd_refined 0.18 r_symmetry_vdw_refined 0.171 r_symmetry_hbond_refined 0.135 r_xyhbond_nbd_refined 0.096 r_chiral_restr 0.088 r_bond_refined_d 0.01 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 6604 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement CNS refinement HKL-3000 data collection DENZO data reduction SCALEPACK data scaling CNS phasing