1N5L

CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE CRYSTALLIZED IN SODIUM MALONATE, AFTER CATALYSIS IN THE CRYSTAL (2.3 A RESOLUTION)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1N5KPDB ENTRY 1N5K

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP, STREAK SEEDING, SOAKING62931.4 M sodium malonate, 2% PEG 2000, 0.1 M MES pH 6.0, 2 mM b-mercaptoethanol, 25 mM magnesium acetate, soaking in 30 mM ATP, VAPOR DIFFUSION, HANGING DROP, STREAK SEEDING, SOAKING
Crystal Properties
Matthews coefficientSolvent content
2.6453.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.454α = 90
b = 64.454β = 90
c = 195.899γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42001-04-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.936ESRFID29

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
12.319.7699.40.1074.66.92164821648-341
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)
2.32.421000.3811.97.22977

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 DIFFRACTIONOTHERTHROUGHOUTPDB ENTRY 1N5K2.319.762157721577105499.10.2380.2360.2360.28RANDOM35.9
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]
6.084.76.08-12.17
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21
c_scangle_it6.32
c_mcangle_it5.31
c_scbond_it5.06
c_mcbond_it3.41
c_angle_deg1.5
c_improper_angle_d1.09
c_bond_d0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2905
Nucleic Acid Atoms
Solvent Atoms205
Heterogen Atoms63

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4data scaling
CNSphasing