1N5J

CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE DIPHOSPHATE (TDP) AND THYMIDINE TRIPHOSPHATE (TTP) AT PH 5.4 (1.85 A RESOLUTION)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GSI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.4293Soaking in 30mM ATP, 40% PEG 2000, 10 mM ammonium sulphate, 0.1 M MES pH 5.4, 25 mM magnesium acetate, 2 mM mercaptoethanol, 3 mM EDTA, 1.5 mM DTT, VAPOR DIFFUSION, HANGING DROP + SOAKING
Crystal Properties
Matthews coefficientSolvent content
2.2945.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.248α = 90
b = 76.248β = 90
c = 135.114γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2001-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.90ESRFBM30A

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
11.8524.9694.10.05564.71906319063-316.6
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)
1.851.9594.10.3162.34.62788

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 DIFFRACTIONOTHERTHROUGHOUT1GSI1.8524.96190471904792992.60.2150.2150.2150.226RANDOM19.2
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]
1.882.081.88-3.77
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d20.8
c_scangle_it3.66
c_scbond_it2.89
c_mcangle_it1.5
c_angle_deg1.1
c_mcbond_it1.04
c_improper_angle_d0.73
c_bond_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1546
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms66

Software

Software
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
CNSrefinement
CCP4data scaling
CNSphasing