5ZAX

Crystal structure of thymidylate kinase in complex with ADP, TDP and TMP from thermus thermophilus HB8

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		295	0.2M MgCl2.6H2O, 0.1M Tris hydrochloride, 30% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.408	α = 90
b = 47.658	β = 90
c = 152.329	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate		2013-07-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU ULTRAX 18	1.54179

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	2.36	18.54	99.7	0.135	0.995	10.5	7		14849

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.36	2.46			0.453	0.847

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	5X7J	2.36	18.54	13923	688	98.29	0.2488	0.2451	0.3239	RANDOM	19.868

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]
1.23			-0.86		-0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.163
r_dihedral_angle_4_deg	16.572
r_dihedral_angle_3_deg	14.608
r_dihedral_angle_1_deg	5.18
r_angle_other_deg	3.604
r_mcangle_it	1.439
r_angle_refined_deg	1.349
r_mcbond_it	0.791
r_mcbond_other	0.789
r_chiral_restr	0.063

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.163
r_dihedral_angle_4_deg	16.572
r_dihedral_angle_3_deg	14.608
r_dihedral_angle_1_deg	5.18
r_angle_other_deg	3.604
r_mcangle_it	1.439
r_angle_refined_deg	1.349
r_mcbond_it	0.791
r_mcbond_other	0.789
r_chiral_restr	0.063
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_gen_planes_other	0.005
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2907
Nucleic Acid Atoms
Solvent Atoms	58
Heterogen Atoms	85

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.