2AF6

Crystal structure of Mycobacterium tuberculosis Flavin dependent thymidylate synthase (Mtb ThyX) in the presence of co-factor FAD and substrate analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (BrdUMP)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1O26PDB ENTRY 1O26

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.5298100mM Sodium acetate, 200mM potassium iodide, 2mM DTT and PEG3350, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.2645.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.09α = 90
b = 78.3β = 96.8
c = 168.72γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102004-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.10.9794ALS8.2.1

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
12.01344.9596.10.09611.43.413286913286920.73
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)
122.07890.4743.12.912213

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 DIFFRACTIONSAD in combination with Molecular ReplacementTHROUGHOUTPDB ENTRY 1O262.0144.95132869126330650695.470.19780.19780.195480.24292RANDOM24.695
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.286
r_dihedral_angle_4_deg18.014
r_dihedral_angle_3_deg14.934
r_dihedral_angle_1_deg5.441
r_scangle_it2.568
r_scbond_it1.667
r_angle_refined_deg1.293
r_mcangle_it1.139
r_mcbond_it0.681
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.286
r_dihedral_angle_4_deg18.014
r_dihedral_angle_3_deg14.934
r_dihedral_angle_1_deg5.441
r_scangle_it2.568
r_scbond_it1.667
r_angle_refined_deg1.293
r_mcangle_it1.139
r_mcbond_it0.681
r_nbtor_refined0.3
r_symmetry_hbond_refined0.286
r_nbd_refined0.208
r_symmetry_vdw_refined0.194
r_xyhbond_nbd_refined0.16
r_metal_ion_refined0.126
r_chiral_restr0.082
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15074
Nucleic Acid Atoms
Solvent Atoms989
Heterogen Atoms686

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
AMoREphasing