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Crystal Structure at 1.8 Angstrom of CDP-D-glucose 4,6-dehydratase from Yersinia pseudotuberculosis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 ammonium sulfate, PEG 4000, potassium HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.3 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.9 α = 90 b = 115.87 β = 90 c = 126.83 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 113 CCD ADSC QUANTUM 4 1999-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12B 1.0704 NSLS X12B
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 1.8 50 97.7 0.066 18.4 5.8 136502 133360 2 19.8
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) 1.8 1.86 93.4 0.35 2.6 3.2 13502
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 MAD + MIR THROUGHOUT NONE 1.8 36.25 133248 133248 5025 97.5 0.229 0.229 0.229 0.229 0.266 0.2661 SHELLS 27
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] 8.04 -3.89 -4.16
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21 c_scangle_it 5.17 c_mcangle_it 3.23 c_scbond_it 3.1 c_mcbond_it 2.22 c_angle_deg 1.2 c_improper_angle_d 0.74 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21 c_scangle_it 5.17 c_mcangle_it 3.23 c_scbond_it 3.1 c_mcbond_it 2.22 c_angle_deg 1.2 c_improper_angle_d 0.74 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11121 Nucleic Acid Atoms Solvent Atoms 862 Heterogen Atoms 176
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling MLPHARE phasing