5UIV

Structure of Thymidylate Kinase from Candida albicans Reveals Origin of Broad Substrate Specificity and a Novel Structural Element.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2850.1 M HEPES, 1.1 N Sodium Citrate, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
3.1761.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.965α = 90
b = 69.965β = 90
c = 116.161γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442015-08-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E DW1.54178

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
12.4560.5992.10.1341.892.911717
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)
12.452.550.278

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3tmk2.4560.591105660692.090.170490.167880.21805RANDOM36.429
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]
0.010.010.01-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.321
r_dihedral_angle_4_deg18.711
r_dihedral_angle_3_deg15.075
r_long_range_B_refined7.221
r_long_range_B_other7.196
r_dihedral_angle_1_deg6.207
r_scangle_other5.557
r_mcangle_it4.349
r_mcangle_other4.348
r_scbond_it3.564
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.321
r_dihedral_angle_4_deg18.711
r_dihedral_angle_3_deg15.075
r_long_range_B_refined7.221
r_long_range_B_other7.196
r_dihedral_angle_1_deg6.207
r_scangle_other5.557
r_mcangle_it4.349
r_mcangle_other4.348
r_scbond_it3.564
r_scbond_other3.562
r_mcbond_it2.861
r_mcbond_other2.858
r_angle_refined_deg1.938
r_angle_other_deg1.039
r_chiral_restr0.101
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms1817
Nucleic Acid Atoms
Solvent Atoms77
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing