3N2I | pdb_00003n2i

2.25 Angstrom resolution crystal structure of a thymidylate kinase (tmk) from Vibrio cholerae O1 biovar eltor str. N16961 in complex with thymidine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3LV8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	295	7.0 mg/mL protein in 10 mM Tris/HCl pH 8.3 0.25 M NaCl, 5 mM BME. Crystallization condition is The PACT Suite (#34). Crystals grew from 1:1 v/v drop, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.6	α = 90
b = 92.6	β = 90
c = 231.538	γ = 90

Symmetry
Space Group	I 41 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	CCD	MARMOSAIC 300 mm CCD	Be Lenses/Diamond Laue Mono	2010-04-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	2.25	30	99.9	0.059	40.13	14.6	24340	24340		-3

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	2.25	2.29	100		0.502	6.3	14.8	1176

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	3LV8	2.25	29.64	23074	23074	1239	99.88	0.20846	0.2058	0.23	0.26109	0.27	RANDOM	69.842

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]
2.26			2.26		-4.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.626
r_dihedral_angle_4_deg	13.196
r_dihedral_angle_3_deg	10.459
r_scangle_it	3.449
r_dihedral_angle_1_deg	2.408
r_scbond_it	2.102
r_angle_refined_deg	1.844
r_mcangle_it	1.173
r_angle_other_deg	0.98
r_mcbond_it	0.631

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.626
r_dihedral_angle_4_deg	13.196
r_dihedral_angle_3_deg	10.459
r_scangle_it	3.449
r_dihedral_angle_1_deg	2.408
r_scbond_it	2.102
r_angle_refined_deg	1.844
r_mcangle_it	1.173
r_angle_other_deg	0.98
r_mcbond_it	0.631
r_mcbond_other	0.165
r_chiral_restr	0.094
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3250
Nucleic Acid Atoms
Solvent Atoms	77
Heterogen Atoms	36

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

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 R01GM157729.