1SJN

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 1SIX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8298PEG 3350, magnesium nitrate, TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4148.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.521α = 90
b = 78.506β = 90
c = 94.509γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152003-11-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.21.1271ALS8.2.2

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
11.89098.80.069204.9399973999732.6
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)
11.81.8699.70.3255.74.93975

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1SIX1.860.863790637906201698.830.170.169730.168230.19765RANDOM24.076
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]
-1.030.910.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.532
r_scangle_it4.863
r_scbond_it2.974
r_mcangle_it1.996
r_angle_refined_deg1.949
r_mcbond_it1.136
r_angle_other_deg0.915
r_symmetry_vdw_other0.313
r_nbd_other0.262
r_symmetry_vdw_refined0.262
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.532
r_scangle_it4.863
r_scbond_it2.974
r_mcangle_it1.996
r_angle_refined_deg1.949
r_mcbond_it1.136
r_angle_other_deg0.915
r_symmetry_vdw_other0.313
r_nbd_other0.262
r_symmetry_vdw_refined0.262
r_symmetry_hbond_refined0.258
r_nbd_refined0.197
r_xyhbond_nbd_refined0.185
r_chiral_restr0.124
r_nbtor_other0.083
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_gen_planes_other0.008
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3037
Nucleic Acid Atoms
Solvent Atoms206
Heterogen Atoms103

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing