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Glycogen Phosphorylase b in complex with (1R)-3'-(2-naphthyl)-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 2.34 47.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.02 α = 90 b = 126.02 β = 90 c = 114.881 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 1.86 30 100 0.048 22.3 5.3 77891 77891 -3 21.3
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) 1.86 1.89 100 0.344 5.9 5.4
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 1.86 30 73897 3916 99.9 0.19487 0.19356 0.21919 RANDOM 21.827
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] 0.56 0.56 -1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.226 r_dihedral_angle_4_deg 16.529 r_dihedral_angle_3_deg 12.624 r_dihedral_angle_1_deg 5.225 r_scangle_it 1.585 r_scbond_it 0.99 r_angle_refined_deg 0.971 r_mcangle_it 0.719 r_mcbond_it 0.419 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.226 r_dihedral_angle_4_deg 16.529 r_dihedral_angle_3_deg 12.624 r_dihedral_angle_1_deg 5.225 r_scangle_it 1.585 r_scbond_it 0.99 r_angle_refined_deg 0.971 r_mcangle_it 0.719 r_mcbond_it 0.419 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.231 r_nbd_refined 0.182 r_symmetry_hbond_refined 0.141 r_xyhbond_nbd_refined 0.101 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 6624 Nucleic Acid Atoms Solvent Atoms 869 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling