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Characterization of Substrate Binding and Catalysis of the Potential Antibacterial Target N-acetylglucosamine-1-phosphate Uridyltransferase (GlmU)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VOI PDB ENTRY 2VOI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 pH 6.0
Crystal Properties Matthews coefficient Solvent content 3.43 63.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.72 α = 90 b = 108.72 β = 90 c = 326.754 γ = 120
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 ADSC CCD 2003-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID APS 17-ID
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 50 90.2 0.06 23.1 4.9 45786
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 2.07 91.3 0.3 4.5
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 PDB ENTRY 2VOI 2 20 42985 2307 89.5 0.199 0.197 0.2143 0.223 0.239 RANDOM 22.11
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] 0.63 0.31 0.63 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.908 r_dihedral_angle_4_deg 17.427 r_dihedral_angle_3_deg 13.016 r_dihedral_angle_1_deg 5.914 r_scangle_it 1.408 r_angle_refined_deg 1.234 r_mcangle_it 1.104 r_angle_other_deg 1.065 r_scbond_it 0.986 r_mcbond_it 0.916
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.908 r_dihedral_angle_4_deg 17.427 r_dihedral_angle_3_deg 13.016 r_dihedral_angle_1_deg 5.914 r_scangle_it 1.408 r_angle_refined_deg 1.234 r_mcangle_it 1.104 r_angle_other_deg 1.065 r_scbond_it 0.986 r_mcbond_it 0.916 r_symmetry_vdw_other 0.238 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.194 r_nbd_other 0.177 r_nbtor_refined 0.161 r_symmetry_hbond_refined 0.158 r_xyhbond_nbd_refined 0.143 r_nbtor_other 0.081 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3406 Nucleic Acid Atoms Solvent Atoms 361 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement HKL-2000 phasing