5FUW

catalytic domain of Thymidine kinase from Trypanosoma brucei with dTMP or dThd

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5FUV	PDB ENTRY 5FUV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		0.1 M HEPES PH 7.0, 0.8 M SUCCINIC ACID 1 MM TMP, 1 MM APPNHP, 3 MM MGCL2

Crystal Properties
Matthews coefficient	Solvent content
3.77	67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.999	α = 90
b = 114.999	β = 90
c = 104.77	γ = 90

Symmetry
Space Group	P 43 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100					M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02		Diamond	I02

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	2.2	64.24	100	0.1	11.8	11.6		36299		2

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	2.2	2.27	100		0.88	2.6	10.8

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	PDB ENTRY 5FUV	2.2	115	34470	1757	99.88	0.1861	0.18532	0.20126	RANDOM	55.707

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			-1.23		2.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.005
r_dihedral_angle_3_deg	12.572
r_long_range_B_refined	12.472
r_long_range_B_other	12.472
r_dihedral_angle_4_deg	11.105
r_scangle_other	10.463
r_mcangle_it	7.817
r_mcangle_other	7.815
r_scbond_it	7.574
r_scbond_other	7.409
r_dihedral_angle_1_deg	6.675
r_mcbond_it	5.71
r_mcbond_other	5.706
r_angle_refined_deg	2.16
r_angle_other_deg	1.636
r_chiral_restr	0.125
r_bond_refined_d	0.022
r_gen_planes_refined	0.013
r_bond_other_d	0.009
r_gen_planes_other	0.008
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	2577
Nucleic Acid Atoms
Solvent Atoms	147
Heterogen Atoms	55

Software

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