☰ Navigation Tabs
1.05 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Acinetobacter baumannii in Covalently Bound Complex with (2R)-2-(phosphonooxy)propanoic Acid.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BQ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 Protein: 17.2 mg/ml, 0.5M Sodium chloride, 0.01M Tris-HCL (pH 8.3);
Screen: JCSG+ (F8), 2.1M DL-Malic acid (pH 7.0);
Cryo: 4M Sodium formate.
Crystal Properties Matthews coefficient Solvent content 2.08 40.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.289 α = 90 b = 70.085 β = 110.05 c = 78.109 γ = 90
Symmetry Space Group P 1 21 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 C(111) 2016-06-30 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) 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 1.05 20 99.5 0.064 0.064 16.9 4 357259 -3 7.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.05 1.07 99.4 0.625 0.919 2.5 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT 5BQ2 1.05 19.96 338746 17929 99.38 0.16226 0.16156 0.1675 0.17561 0.1819 RANDOM 11.965
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] -0.18 -0.13 -0.09 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.895 r_sphericity_free 17.23 r_dihedral_angle_4_deg 11.16 r_dihedral_angle_3_deg 11.025 r_sphericity_bonded 4.943 r_dihedral_angle_1_deg 4.47 r_long_range_B_refined 1.862 r_long_range_B_other 1.862 r_angle_refined_deg 1.458 r_rigid_bond_restr 1.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.895 r_sphericity_free 17.23 r_dihedral_angle_4_deg 11.16 r_dihedral_angle_3_deg 11.025 r_sphericity_bonded 4.943 r_dihedral_angle_1_deg 4.47 r_long_range_B_refined 1.862 r_long_range_B_other 1.862 r_angle_refined_deg 1.458 r_rigid_bond_restr 1.159 r_angle_other_deg 0.84 r_scangle_other 0.835 r_scbond_it 0.649 r_scbond_other 0.649 r_mcangle_it 0.568 r_mcangle_other 0.568 r_mcbond_it 0.398 r_mcbond_other 0.398 r_chiral_restr 0.088 r_gen_planes_refined 0.021 r_gen_planes_other 0.018 r_bond_refined_d 0.008 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6286 Nucleic Acid Atoms Solvent Atoms 1197 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing