5EDD

Crystal structure of Mycobacterium tuberculosis dUTPase R140K, H145W mutant


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2931.5 M ammonium sulfate, 0.1M Tris/HCl, 12% glycerol, 6.7 mM dUPnPP, 20 mM magnesium chloride
Crystal Properties
Matthews coefficientSolvent content
2.0439.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.052α = 90
b = 55.052β = 90
c = 83.827γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDAGILENT EOS CCD2013-09-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEOTHER1.54056

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
11.9741.9199.80.136.13.511022010220
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)
11.972.081000.4971.62.5

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT3HZA1.9741.91969049599.560.162370.159940.21108RANDOM21.018
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]
0.030.010.03-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.434
r_dihedral_angle_4_deg17.977
r_dihedral_angle_1_deg14.529
r_dihedral_angle_3_deg12.356
r_long_range_B_refined5.586
r_long_range_B_other5.043
r_scangle_other2.757
r_mcangle_it2.218
r_mcangle_other2.217
r_angle_refined_deg2.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.434
r_dihedral_angle_4_deg17.977
r_dihedral_angle_1_deg14.529
r_dihedral_angle_3_deg12.356
r_long_range_B_refined5.586
r_long_range_B_other5.043
r_scangle_other2.757
r_mcangle_it2.218
r_mcangle_other2.217
r_angle_refined_deg2.005
r_scbond_other1.819
r_scbond_it1.814
r_mcbond_it1.433
r_mcbond_other1.412
r_angle_other_deg0.938
r_chiral_restr0.103
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1026
Nucleic Acid Atoms
Solvent Atoms159
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
Cootmodel building