1XBT | pdb_00001xbt

Crystal Structure of Human Thymidine Kinase 1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	288	sodium citrate, 2-propanol, PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K

Crystal Properties
Matthews coefficient	Solvent content
3	58.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 157.672	α = 90
b = 123.177	β = 130.2
c = 116	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	ADSC QUANTUM 4		2003-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.25	87.7	28.4	0.101	4.9	3.5	77566	77566	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.25	2.37	98.6		0.434	1.5	3.5	11361

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SIRAS	THROUGHOUT	2.4	42.07	62088	3317	98.92	0.20288	0.20133	0.2	0.23204	0.23	RANDOM	34.695

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]
2.86		1.78	-0.5		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.619
r_scangle_it	2.541
r_scbond_it	1.461
r_angle_refined_deg	1.259
r_mcangle_it	1.024
r_mcbond_it	0.519
r_metal_ion_refined	0.235
r_nbd_refined	0.184
r_symmetry_vdw_refined	0.176
r_xyhbond_nbd_refined	0.143
r_symmetry_hbond_refined	0.11
r_chiral_restr	0.088
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_mcbond_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	213
Heterogen Atoms	248

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
autoSHARP	phasing