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2.3 Angstrom Crystal Structure of 3-deoxy-manno-octulosonate Cytidylyltransferase (kdsB) from Acinetobacter baumannii.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VH1 PDB entry 1VH1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 Protein: 7mg/mL, 0.1M Sodium cloride, Tris-HCl (pH 8.3);
Screen: Classics II (D7), 0.1M Bis-Tris pH 6.5, 25% (w/v) PEG 3350. , VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.97 37.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.702 α = 90 b = 40.832 β = 97.23 c = 56.491 γ = 90
Symmetry Space Group C 1 2 1
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 MARMOSAIC 225 mm CCD Beryllium lenses 2010-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.3 30 98.7 0.08 15.3 3.7 11015 11015 -3 39.3
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 2.3 2.34 100 0.331 4 3.7 548
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 1VH1 2.3 28.02 9822 9822 1073 98.68 0.18052 0.18052 0.17586 0.1779 0.22275 0.2168 RANDOM 35.236
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] -0.41 2.73 -1.44 2.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.775 r_dihedral_angle_4_deg 15.625 r_dihedral_angle_3_deg 10.36 r_scangle_it 5.863 r_scbond_it 3.652 r_dihedral_angle_1_deg 3.017 r_mcangle_it 2.231 r_angle_refined_deg 1.489 r_mcbond_it 1.266 r_angle_other_deg 0.843
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.775 r_dihedral_angle_4_deg 15.625 r_dihedral_angle_3_deg 10.36 r_scangle_it 5.863 r_scbond_it 3.652 r_dihedral_angle_1_deg 3.017 r_mcangle_it 2.231 r_angle_refined_deg 1.489 r_mcbond_it 1.266 r_angle_other_deg 0.843 r_mcbond_other 0.339 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2066 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling