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Crystal structure of yeast glycogen synthase in complex with uridine-5'-monophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NB0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.2 298 0.1 M Bis-Tris, 16% PEG 300, pH 6.2, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.1 60.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 193.089 α = 90 b = 204.372 β = 90 c = 206.446 γ = 90
Symmetry Space Group I 2 2 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 ADSC QUANTUM 315r 2012-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.98 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.66 50 95 0.081 11.1 5.7 117070 111217 0.2 69.509583
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.66 2.71 88.4 0.66 4.4 5125
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3NB0 2.66 48.46 111215 5574 94.96 0.2111 0.2085 0.207 0.2601 0.2593 RANDOM 80.9411
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] -4.23 9.42 -5.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.153 r_dihedral_angle_4_deg 19.253 r_dihedral_angle_3_deg 18.59 r_dihedral_angle_1_deg 5.627 r_angle_refined_deg 1.277 r_chiral_restr 0.088 r_bond_refined_d 0.008 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20563 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 176
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing