3LV8 | pdb_00003lv8

1.8 Angstrom resolution crystal structure of a thymidylate kinase (tmk) from Vibrio cholerae O1 biovar eltor str. N16961 in complex with TMP, thymidine-5'-diphosphate and ADP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4TMK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	295	7mg/mL protein; The PACT Suite condition #47 (D11), pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.973	α = 90
b = 112.973	β = 90
c = 112.973	γ = 90

Symmetry
Space Group	P 43 3 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 225 mm CCD	Beryllium lenses	2010-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	1.8	30	99.5	0.071	28.3	10	23299	23299		-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	1.8	1.83	95.3		0.426	3.8	6.2	1089

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	4TMK	1.8	30	22043	22043	1196	99.44	0.16611	0.1641	0.19	0.20393	0.23	RANDOM	24.439

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.691
r_dihedral_angle_4_deg	11.355
r_dihedral_angle_3_deg	10.281
r_scangle_it	3.541
r_dihedral_angle_1_deg	2.919
r_scbond_it	2.235
r_angle_refined_deg	1.494
r_mcangle_it	1.322
r_angle_other_deg	0.835
r_mcbond_it	0.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.691
r_dihedral_angle_4_deg	11.355
r_dihedral_angle_3_deg	10.281
r_scangle_it	3.541
r_dihedral_angle_1_deg	2.919
r_scbond_it	2.235
r_angle_refined_deg	1.494
r_mcangle_it	1.322
r_angle_other_deg	0.835
r_mcbond_it	0.73
r_mcbond_other	0.217
r_chiral_restr	0.086
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1601
Nucleic Acid Atoms
Solvent Atoms	287
Heterogen Atoms	80

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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.