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Ser162 mutant of glycogenin complexed with UDP-glucose and manganese
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LL3 PDB ENTRY 1LL3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 293 sodium MES, ammonium sulfate, PEG MME 5000, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.4 47.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.89 α = 90 b = 105.38 β = 90 c = 122.21 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 93 IMAGE PLATE RIGAKU RAXIS IV 2003-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2.45 33 99.4 0.063 21.7 5.9 14347 14237 0.2 0.2 45.8
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 2.45 2.54 93.8 93.8 0.218 5.6
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-Factor (All) 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 PDB ENTRY 1LL3 2.45 33 14349 14072 706 98.1 0.251 0.2 0.199 0.1902 0.217 0.2042 random 40.575
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] -16.612 5.079 11.533
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.61 c_scangle_it 3.25 c_mcangle_it 2.529 c_scbond_it 2.157 c_mcbond_it 1.479 c_angle_d 1.2 c_improper_angle_d 1.14 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2049 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 39
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement PDB_EXTRACT data extraction CNS phasing