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1.9 Angstrom Crystal Structure of 3-deoxy-manno-octulosonate Cytidylyltransferase (kdsB) from Acinetobacter baumannii without His-Tag Bound to the Active Site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3POL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 295 Protein: 7.4mG/mL, 0.25M Sodium cloride, Tris-HCl (pH 8.3), Screen: JCSG+ (H8), 0.2M Sodium chloride, 0.1M Bis-Tris pH 5.5, 25% (w/v) PEG 3350., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.04 39.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.542 α = 90 b = 40.155 β = 103.6 c = 54.71 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 300 mm CCD Beryllium lenses 2012-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 30 99.8 0.091 13.3 3.7 18315 18315 -3 22
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 1.93 99.3 0.49 2.5 3.4 909
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 3POL 1.9 29.52 17342 17342 940 99.78 0.18999 0.18999 0.18719 0.1928 0.24233 0.25 RANDOM 22.357
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] -0.28 1.17 -1.56 2.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.672 r_dihedral_angle_4_deg 12.67 r_dihedral_angle_3_deg 11.064 r_scangle_it 5.034 r_scbond_it 3.076 r_dihedral_angle_1_deg 2.945 r_mcangle_it 1.917 r_angle_refined_deg 1.415 r_mcbond_it 1.129 r_angle_other_deg 0.851
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.672 r_dihedral_angle_4_deg 12.67 r_dihedral_angle_3_deg 11.064 r_scangle_it 5.034 r_scbond_it 3.076 r_dihedral_angle_1_deg 2.945 r_mcangle_it 1.917 r_angle_refined_deg 1.415 r_mcbond_it 1.129 r_angle_other_deg 0.851 r_mcbond_other 0.345 r_chiral_restr 0.087 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 1993 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling