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2.0 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Streptococcus pneumoniae in Complex with Uridine-diphosphate-2(n-acetylglucosaminyl) butyric acid, (2R)-2-(phosphonooxy)propanoic acid and Magnesium.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SG1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 Protein: 8.2 mg/ml, 0.01M Tris HCl (pH 8.3);
Screen: PACT (B4), 0.01M MIB buffer (pH 7.0), 25% (w/v) PEG 1500.
Crystal Properties Matthews coefficient Solvent content 2.2 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.243 α = 90 b = 80.13 β = 95.76 c = 126.511 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) 2017-07-12 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) Rpim I (All) 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 30 100 0.076 0.076 0.04 18.9 4.5 113220 -3 30.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 100 0.756 0.756 0.405 0.697 2.03 4.4
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 3SG1 2 29.29 107143 5833 99.73 0.22457 0.22225 0.2279 0.26625 0.2712 RANDOM 50.996
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] 2.3 0.14 -2.21 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.214 r_dihedral_angle_4_deg 14.977 r_dihedral_angle_3_deg 11.922 r_long_range_B_other 9.523 r_long_range_B_refined 9.517 r_scangle_other 7.067 r_mcangle_it 6.767 r_mcangle_other 6.767 r_mcbond_other 4.808 r_mcbond_it 4.807
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.214 r_dihedral_angle_4_deg 14.977 r_dihedral_angle_3_deg 11.922 r_long_range_B_other 9.523 r_long_range_B_refined 9.517 r_scangle_other 7.067 r_mcangle_it 6.767 r_mcangle_other 6.767 r_mcbond_other 4.808 r_mcbond_it 4.807 r_scbond_it 4.719 r_scbond_other 4.719 r_dihedral_angle_1_deg 3.036 r_angle_refined_deg 1.518 r_angle_other_deg 0.886 r_chiral_restr 0.088 r_gen_planes_refined 0.022 r_gen_planes_other 0.02 r_bond_refined_d 0.01 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12687 Nucleic Acid Atoms Solvent Atoms 637 Heterogen Atoms 220
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MoRDa phasing