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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 2V0H PDB ENTRY 2V0H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 1.2-1.8M AMMONIUM SULFATE, 2%PEG-400, 0.1M MES PH 5.2-6.1, 20 MM MGCL2, 10 MM UDP-GLCNAC
Crystal Properties Matthews coefficient Solvent content 3.65 66.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.808 α = 90 b = 107.808 β = 90 c = 233.876 γ = 120
Symmetry Space Group P 63 2 2
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 1.9 50 99.1 0.07 37.9 9 64262
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 1.97 99.9 0.32 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 2V0H 1.89 119.52 60974 3260 98.3 0.194 0.193 0.202 0.21 0.2207 RANDOM 21.81
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] 1.25 0.62 1.25 -1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.74 r_scangle_it 3.371 r_scbond_it 1.954 r_angle_refined_deg 1.266 r_mcangle_it 1.123 r_angle_other_deg 1.047 r_mcbond_it 0.565 r_symmetry_vdw_other 0.319 r_nbd_other 0.238 r_symmetry_vdw_refined 0.192
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.74 r_scangle_it 3.371 r_scbond_it 1.954 r_angle_refined_deg 1.266 r_mcangle_it 1.123 r_angle_other_deg 1.047 r_mcbond_it 0.565 r_symmetry_vdw_other 0.319 r_nbd_other 0.238 r_symmetry_vdw_refined 0.192 r_nbd_refined 0.191 r_symmetry_hbond_refined 0.188 r_xyhbond_nbd_refined 0.121 r_chiral_restr 0.116 r_nbtor_other 0.083 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d 0.003 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined 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 3415 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing