2WVJ | pdb_00002wvj

Mutation of Thr163 to Ser in Human Thymidine Kinase Shifts the Specificity from Thymidine towards the Nucleoside Analogue Azidothymidine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XBT	PDB ENTRY 1XBT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6		HANGING DROPS WITH EQUAL AMOUNTS OF PROTEIN, 10 MG PER ML CONTAINING 5 MM TTP AND TRAY SOLUTION COMPOSED OF SODIUM CITRATE PH 5.6, 2-PROPANOL AND PEG 4000.

Crystal Properties
Matthews coefficient	Solvent content
2.7	43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 156.902	α = 90
b = 123.252	β = 132.98
c = 121.024	γ = 90

Symmetry
Space Group	C 1 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	MARRESEARCH		2007-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2		ESRF	ID23-2

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	88.39	99.9	0.1	10.56	3.7		85203		-3.7	24.5

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	2.22	99.9		0.37	3.4	3.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1XBT	2.2	49.814	85195	4263	99.857	0.176	0.1733	0.17	0.2209	0.22	RANDOM	21.101

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]
-0.232		-0.268	-0.069		-0.065

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.468
r_dihedral_angle_4_deg	20.35
r_dihedral_angle_3_deg	15.446
r_dihedral_angle_1_deg	5.919
r_scangle_it	1.846
r_angle_refined_deg	1.215
r_scbond_it	1.115
r_mcangle_it	0.789
r_mcbond_it	0.441
r_nbtor_refined	0.301
r_symmetry_vdw_refined	0.208
r_nbd_refined	0.182
r_xyhbond_nbd_refined	0.15
r_symmetry_hbond_refined	0.127
r_chiral_restr	0.085
r_metal_ion_refined	0.055
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9990
Nucleic Acid Atoms
Solvent Atoms	1074
Heterogen Atoms	243

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing