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Glycogen Phosphorylase b in complex with (1R)-3'-(4-methoxyphenyl)-spiro[1,5-anhydro-D-glucitol-1,5'-isoxazoline]
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 10 mM Bes buffer, 3 mM DDT , pH 6.7, SMALL TUBES, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.47 50.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.816 α = 90 b = 128.816 β = 90 c = 116.199 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 ADSC QUANTUM 4 2006-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 0.979 SRS PX9.6
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 1.85 30 98.9 0.056 16.4 5.2 82746 82746 -3 24.5
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) 1.85 1.88 98.1 0.433 4.7 5
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT pdb entry 2PRJ 1.85 30 78563 4126 98.92 0.19057 0.1895 0.21097 RANDOM 27.498
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] 0.72 0.72 -1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.042 r_dihedral_angle_4_deg 18.823 r_dihedral_angle_3_deg 14.496 r_dihedral_angle_1_deg 5.054 r_scangle_it 1.909 r_scbond_it 1.186 r_angle_refined_deg 0.989 r_mcangle_it 0.855 r_mcbond_it 0.501 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.042 r_dihedral_angle_4_deg 18.823 r_dihedral_angle_3_deg 14.496 r_dihedral_angle_1_deg 5.054 r_scangle_it 1.909 r_scbond_it 1.186 r_angle_refined_deg 0.989 r_mcangle_it 0.855 r_mcbond_it 0.501 r_nbtor_refined 0.303 r_nbd_refined 0.18 r_symmetry_vdw_refined 0.158 r_xyhbond_nbd_refined 0.085 r_chiral_restr 0.071 r_symmetry_hbond_refined 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6609 Nucleic Acid Atoms Solvent Atoms 372 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling