3NWY

Structure and allosteric regulation of the uridine monophosphate kinase from Mycobacterium tuberculosis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherin-house model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.7291Na/K Tartrate 1.1 M HEPES pH 7.7 0.1 M MPD 2%, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.2144.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.71α = 90
b = 175.48β = 90
c = 65.41γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-02-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.918500ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.4787.790.80.1210.04412.24.2573845189911
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.492.661.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTin-house model2.5487.75319443188237286.110.208130.204740.26859RANDOM43.273
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]
0.72-1.130.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.63
r_dihedral_angle_4_deg23.843
r_dihedral_angle_3_deg21.686
r_dihedral_angle_1_deg7.148
r_scangle_it1.916
r_angle_refined_deg1.402
r_scbond_it1.136
r_mcangle_it0.932
r_angle_other_deg0.915
r_mcbond_it0.506
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.63
r_dihedral_angle_4_deg23.843
r_dihedral_angle_3_deg21.686
r_dihedral_angle_1_deg7.148
r_scangle_it1.916
r_angle_refined_deg1.402
r_scbond_it1.136
r_mcangle_it0.932
r_angle_other_deg0.915
r_mcbond_it0.506
r_chiral_restr0.076
r_mcbond_other0.065
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9987
Nucleic Acid Atoms
Solvent Atoms142
Heterogen Atoms217

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling