5UIV

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3TMK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		285	0.1 M HEPES, 1.1 N Sodium Citrate, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.965	α = 90
b = 69.965	β = 90
c = 116.161	γ = 120

Symmetry
Space Group	P 32 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RIGAKU SATURN 944		2015-08-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E DW	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.45	60.59	92.1	0.134	1.89	2.9		11717

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.45	2.55			0.278

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3tmk	2.45	60.59	11056	606	92.09	0.17049	0.16788	0.21805	RANDOM	36.429

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]
0.01	0.01		0.01		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.321
r_dihedral_angle_4_deg	18.711
r_dihedral_angle_3_deg	15.075
r_long_range_B_refined	7.221
r_long_range_B_other	7.196
r_dihedral_angle_1_deg	6.207
r_scangle_other	5.557
r_mcangle_it	4.349
r_mcangle_other	4.348
r_scbond_it	3.564
r_scbond_other	3.562
r_mcbond_it	2.861
r_mcbond_other	2.858
r_angle_refined_deg	1.938
r_angle_other_deg	1.039
r_chiral_restr	0.101
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002
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 Atoms	Number
Protein Atoms	1817
Nucleic Acid Atoms
Solvent Atoms	77
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing