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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 1HV9 PDB ENTRY 1HV9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 1.2-1.8M AMMONIUM SULFATE, 2% PEG-400, 0.1M MES PH 5.2 TO 6.5, AND COBALT (II) CHLORIDE 6.25 MM
Crystal Properties Matthews coefficient Solvent content 3.33 62.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.459 α = 90 b = 108.459 β = 90 c = 327.154 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 1.8 50 95.1 0.05 29 4.3 67671
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 1.8 1.84 74.8 0.31 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 PDB ENTRY 1HV9 1.79 111.8 64247 3424 95.9 0.192 0.191 0.2 0.214 0.2175 RANDOM 19.93
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] 0.52 0.26 0.52 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.668 r_scangle_it 2.008 r_scbond_it 1.137 r_angle_other_deg 1.09 r_angle_refined_deg 1.001 r_mcangle_it 0.696 r_mcbond_it 0.348 r_symmetry_vdw_other 0.273 r_nbd_other 0.219 r_nbd_refined 0.176
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.668 r_scangle_it 2.008 r_scbond_it 1.137 r_angle_other_deg 1.09 r_angle_refined_deg 1.001 r_mcangle_it 0.696 r_mcbond_it 0.348 r_symmetry_vdw_other 0.273 r_nbd_other 0.219 r_nbd_refined 0.176 r_symmetry_hbond_refined 0.134 r_chiral_restr 0.106 r_symmetry_vdw_refined 0.104 r_xyhbond_nbd_refined 0.103 r_nbtor_other 0.078 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 3413 Nucleic Acid Atoms Solvent Atoms 497 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing