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Crystal Structure of the nucleoside-diphosphate-sugar pyrophosphorylase from Vibrio cholerae RC9. Northeast Structural Genomics Consortium (NESG) Target VcR193.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Microbatch crystallization under oil 7.5 277 Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 20% PEG 8000, 0.1M magnesium nitrate, 0.1M HEPES, pH 7.5, Microbatch crystallization under oil , temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.07 59.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.303 α = 90 b = 117.003 β = 90 c = 128.561 γ = 90
Symmetry Space Group P 21 21 21
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 2012-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4C 0.97915 NSLS X4C
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 1.9 50 99.9 0.13 25.44 10.4 111486 111375 26.49
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 1.9 1.97 100 0.535 3.16 9.1 11100
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 SAD THROUGHOUT 1.9 37.247 1.24 111069 5653 99.21 0.185 0.184 0.1818 0.203 0.1992 RANDOM 32.746
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] -3.598 3.088 0.51
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.137 f_angle_d 1.334 f_chiral_restr 0.099 f_bond_d 0.008 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3960 Nucleic Acid Atoms Solvent Atoms 386 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction HKL-2000 data scaling SnB phasing