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Glycogen Phosphorylase b in complex with (1R)-3'-(4-methylphenyl)-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
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 2.33 47.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.707 α = 90 b = 125.707 β = 90 c = 114.841 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 1.8 30 97.5 0.037 27 5.2 83355 83355 -3 19.6
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) 1.8 1.83 77.5 0.321 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 ENTRY2PRJ 1.8 30 79094 4161 97.35 0.20034 0.19877 0.22956 RANDOM 18.843
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] 0.53 0.53 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.755 r_dihedral_angle_4_deg 16.763 r_dihedral_angle_3_deg 12.099 r_dihedral_angle_1_deg 5.199 r_scangle_it 1.568 r_scbond_it 0.978 r_angle_refined_deg 0.969 r_mcangle_it 0.684 r_mcbond_it 0.401 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.755 r_dihedral_angle_4_deg 16.763 r_dihedral_angle_3_deg 12.099 r_dihedral_angle_1_deg 5.199 r_scangle_it 1.568 r_scbond_it 0.978 r_angle_refined_deg 0.969 r_mcangle_it 0.684 r_mcbond_it 0.401 r_nbtor_refined 0.304 r_nbd_refined 0.182 r_symmetry_vdw_refined 0.142 r_symmetry_hbond_refined 0.115 r_xyhbond_nbd_refined 0.094 r_chiral_restr 0.068 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6598 Nucleic Acid Atoms Solvent Atoms 897 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling