2V54 | pdb_00002v54

Crystal structure of vaccinia virus thymidylate kinase bound to TDP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1E2G	PDB ENTRY 1E2G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				23% PEG 400, 100 MM NA ACETATE, 100 MM MES PH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.77	α = 90
b = 55.59	β = 90
c = 161.17	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	CCD	ADSC CCD			M	SINGLE WAVELENGTH

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

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	2.4	30	97.2	0.1	12.3	4		79520		-3	46

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	2.4	2.55	93.6		0.59	2.25	4

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 1E2G	2.4	30	20139	1024	97.4	0.2163	0.2163	0.21	0.276	0.27	RANDOM	40.63

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]
0.569			10.451		-11.021

RMS Deviations
Key	Refinement Restraint Deviation
c_angle_deg	1.32742
c_bond_d	0.007289
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3247
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms	60

Software

Software
Software Name	Purpose
CNS	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing