2V0I

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 2V0HPDB ENTRY 2V0H

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
161.2-1.8M AMMONIUM SULFATE, 2%PEG-400, 0.1M MES PH 5.2-6.1, 20 MM MGCL2, 10 MM UDP-GLCNAC
Crystal Properties
Matthews coefficientSolvent content
3.6566.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.808α = 90
b = 107.808β = 90
c = 233.876γ = 120
Symmetry
Space GroupP 63 2 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
11.95099.10.0737.9964262
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)
11.91.9799.90.324.5

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 2V0H1.89119.5260974326098.30.1940.1930.21RANDOM21.81
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]
1.250.621.25-1.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.74
r_scangle_it3.371
r_scbond_it1.954
r_angle_refined_deg1.266
r_mcangle_it1.123
r_angle_other_deg1.047
r_mcbond_it0.565
r_symmetry_vdw_other0.319
r_nbd_other0.238
r_symmetry_vdw_refined0.192
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.74
r_scangle_it3.371
r_scbond_it1.954
r_angle_refined_deg1.266
r_mcangle_it1.123
r_angle_other_deg1.047
r_mcbond_it0.565
r_symmetry_vdw_other0.319
r_nbd_other0.238
r_symmetry_vdw_refined0.192
r_nbd_refined0.191
r_symmetry_hbond_refined0.188
r_xyhbond_nbd_refined0.121
r_chiral_restr0.116
r_nbtor_other0.083
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_gen_planes_other0.004
r_bond_other_d0.003
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 AtomsNumber
Protein Atoms3415
Nucleic Acid Atoms
Solvent Atoms304
Heterogen Atoms102

Software

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