2PY4

Full length structure of the Mycobacterium tuberculosis dUTPase complexed with magnesium and alpha,beta-imido-dUTP.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MQ7pdb entry 1MQ7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52981.5M ammonium sulfate, 0.1M Tris/HCl, 12% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9838.02

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-ray100IMAGE PLATERIGAKU RAXIS IIMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.492094.14.124.573.952158921589-319.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.491.5870.534.83.32.32595

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 REPLACEMENTTHROUGHOUTpdb entry 1MQ71.4919.442048020480110994.090.145530.14420.16997RANDOM18.838
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]
0.060.030.06-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.284
r_dihedral_angle_4_deg16.368
r_dihedral_angle_3_deg9.073
r_dihedral_angle_1_deg6.274
r_scangle_it6.054
r_scbond_it4.976
r_mcangle_it3.137
r_mcbond_it2.164
r_angle_refined_deg1.992
r_nbtor_refined0.321
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.284
r_dihedral_angle_4_deg16.368
r_dihedral_angle_3_deg9.073
r_dihedral_angle_1_deg6.274
r_scangle_it6.054
r_scbond_it4.976
r_mcangle_it3.137
r_mcbond_it2.164
r_angle_refined_deg1.992
r_nbtor_refined0.321
r_nbd_refined0.213
r_symmetry_vdw_refined0.188
r_chiral_restr0.148
r_symmetry_hbond_refined0.147
r_xyhbond_nbd_refined0.108
r_bond_refined_d0.02
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1081
Nucleic Acid Atoms
Solvent Atoms132
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
STARTdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing