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Crystal structure of Glycogen Phosphorylase in complex with glucosyl triazoleacetamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PYD PBD entry 2PYD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SMALL TUBES 6.7 289 10 MM BES BUFFER, 0.1 MM EDTA, 0.02% NAN3, 3 MM DTT, pH 6.7, SMALL TUBES, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.34 47.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.934 α = 90 b = 125.934 β = 90 c = 115.287 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 100 CCD MAR CCD 165 mm 2006-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8073 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.88 30 99.7 0.051 24.5 6.6 75693 71717 -3 21.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.91 100 0.338 6.1 6.7 3680
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PBD entry 2PYD 1.88 30 75693 71717 3802 99.72 0.20176 0.19982 0.23839 RANDOM 22.635
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] 0.7 0.7 -1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.586 r_dihedral_angle_4_deg 16.399 r_dihedral_angle_3_deg 12.461 r_dihedral_angle_1_deg 5.289 r_scangle_it 1.638 r_scbond_it 1.02 r_angle_refined_deg 0.995 r_mcangle_it 0.726 r_mcbond_it 0.427 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.586 r_dihedral_angle_4_deg 16.399 r_dihedral_angle_3_deg 12.461 r_dihedral_angle_1_deg 5.289 r_scangle_it 1.638 r_scbond_it 1.02 r_angle_refined_deg 0.995 r_mcangle_it 0.726 r_mcbond_it 0.427 r_nbtor_refined 0.303 r_nbd_refined 0.182 r_symmetry_vdw_refined 0.152 r_symmetry_hbond_refined 0.136 r_xyhbond_nbd_refined 0.107 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6586 Nucleic Acid Atoms Solvent Atoms 878 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling