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Crystallographic Binding Study of 10 mM N-benzoyl-N'-beta-D-glucopyranosyl urea to glycogen phosphorylase b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HLF PDB ENTRY 1HLF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SMALL TUBES 6.7 287 BES, EDTA, 10mM N-benzoyl-N'-beta-D-glucopyranosyl urea, pH 6.7, SMALL TUBES, temperature 287K
Crystal Properties Matthews coefficient Solvent content 2.47 50.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.519 α = 90 b = 128.519 β = 90 c = 116.497 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 IMAGE PLATE RIGAKU RAXIS IV mirrors 2001-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2.26 28.75 95.8 9.6 10.9 5.3 44261 44361 -3 28
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 2.26 2.3 86.5 42.4 2.6 4.2 1976
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-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1HLF 2.26 28.75 44199 44199 2247 95.8 0.18 0.212 RANDOM 33.5
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]
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 25.1 x_scangle_it 5.65 x_scbond_it 3.65 x_mcangle_it 3.21 x_mcbond_it 2.02 x_angle_deg 1.3 x_improper_angle_d 0.72 x_bond_d 0.007 x_bond_d_na x_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 25.1 x_scangle_it 5.65 x_scbond_it 3.65 x_mcangle_it 3.21 x_mcbond_it 2.02 x_angle_deg 1.3 x_improper_angle_d 0.72 x_bond_d 0.007 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6643 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 61
Software Software Software Name Purpose X-PLOR model building X-PLOR refinement DENZO data reduction SCALEPACK data scaling X-PLOR phasing