3I93

Crystal structure of Mycobacterium tuberculosis dUTPase STOP138T mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HZAPDB entry 3HZA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52931.3 M Ammonium sulfate, 50 mM Tris-HCl, 12 % Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1642.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.591α = 90
b = 54.591β = 90
c = 83.051γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2008-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X120.97861EMBL/DESY, HAMBURGX12

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
11.82099.70.06717.775.5213306-328.165
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)
11.81.8599.20.5032.854.15972

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 3HZA1.819.441199963896.920.166230.164230.20611RANDOM15.958
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]
0.080.040.08-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.01
r_dihedral_angle_4_deg21.334
r_dihedral_angle_3_deg12.003
r_dihedral_angle_1_deg6.754
r_scangle_it4.179
r_scbond_it2.705
r_mcangle_it1.693
r_angle_refined_deg1.549
r_mcbond_it1.017
r_angle_other_deg0.616
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.01
r_dihedral_angle_4_deg21.334
r_dihedral_angle_3_deg12.003
r_dihedral_angle_1_deg6.754
r_scangle_it4.179
r_scbond_it2.705
r_mcangle_it1.693
r_angle_refined_deg1.549
r_mcbond_it1.017
r_angle_other_deg0.616
r_mcbond_other0.324
r_chiral_restr0.077
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_gen_planes_other0.001
r_bond_other_d
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 Atoms1006
Nucleic Acid Atoms
Solvent Atoms105
Heterogen Atoms37

Software

Software
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling