2V0H

Characterization of Substrate Binding and Catalysis of the Potential Antibacterial Target N-acetylglucosamine-1-phosphate Uridyltransferase (GlmU)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HV9PDB ENTRY 1HV9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.51.2-1.8M AMMONIUM SULFATE, 2% PEG-400, 0.1M MES PH 5.2 TO 6.5, AND COBALT (II) CHLORIDE 6.25 MM
Crystal Properties
Matthews coefficientSolvent content
3.3362.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.459α = 90
b = 108.459β = 90
c = 327.154γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2003-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-IDAPS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.85095.10.05294.367671
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8474.80.314

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1HV91.79111.864247342495.90.1920.1910.214RANDOM19.93
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]
0.520.260.52-0.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.668
r_scangle_it2.008
r_scbond_it1.137
r_angle_other_deg1.09
r_angle_refined_deg1.001
r_mcangle_it0.696
r_mcbond_it0.348
r_symmetry_vdw_other0.273
r_nbd_other0.219
r_nbd_refined0.176
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.668
r_scangle_it2.008
r_scbond_it1.137
r_angle_other_deg1.09
r_angle_refined_deg1.001
r_mcangle_it0.696
r_mcbond_it0.348
r_symmetry_vdw_other0.273
r_nbd_other0.219
r_nbd_refined0.176
r_symmetry_hbond_refined0.134
r_chiral_restr0.106
r_symmetry_vdw_refined0.104
r_xyhbond_nbd_refined0.103
r_nbtor_other0.078
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.002
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 AtomsNumber
Protein Atoms3413
Nucleic Acid Atoms
Solvent Atoms497
Heterogen Atoms55

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing