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Crystal structure of UDP-GlcNAc inverting 4,6-dehydratase in complex with NADP and UDP-GlcNAc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SB8 pdb entry 1SB8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 10% (v/v) PEG-200, 100 mM MES, 5% (v/w) PEG-3000, 4% (v/v) acetone, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.51 51.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.846 α = 90 b = 109.846 β = 90 c = 107.978 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 4 2001-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X8C 0.9803 NSLS X8C
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 2.7 50 99.9 0.095 8.8 4.4 20342
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 2.7 2.8 100 0.295 4.3
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 pdb entry 1SB8 2.7 50 19888 1970 97.6 0.204 0.2032 0.269 0.2674 random 32.989
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] -0.078 -5.157 -0.078 0.156
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.708 c_mcangle_it 2.242 c_scbond_it 1.89 c_mcbond_it 1.278
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5163 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 186
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data scaling CNS phasing