1N5L | pdb_00001n5l

CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE CRYSTALLIZED IN SODIUM MALONATE, AFTER CATALYSIS IN THE CRYSTAL (2.3 A RESOLUTION)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1N5K	PDB ENTRY 1N5K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP, STREAK SEEDING, SOAKING	6	293	1.4 M sodium malonate, 2% PEG 2000, 0.1 M MES pH 6.0, 2 mM b-mercaptoethanol, 25 mM magnesium acetate, soaking in 30 mM ATP, VAPOR DIFFUSION, HANGING DROP, STREAK SEEDING, SOAKING

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.454	α = 90
b = 64.454	β = 90
c = 195.899	γ = 120

Symmetry
Space Group	P 31 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		2001-04-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.936	ESRF	ID29

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	2.3	19.76	99.4	0.107	4.6	6.9	21648	21648		-3	41

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)
	2.3	2.42	100		0.381	1.9	7.2	2977

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 (All)	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	OTHER	THROUGHOUT	PDB ENTRY 1N5K	2.3	19.76	21577	21577	1054	99.1	0.238	0.236	0.236	0.22	0.28	0.27	RANDOM	35.9

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]
6.08	4.7		6.08		-12.17

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21
c_scangle_it	6.32
c_mcangle_it	5.31
c_scbond_it	5.06
c_mcbond_it	3.41
c_angle_deg	1.5
c_improper_angle_d	1.09
c_bond_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2905
Nucleic Acid Atoms
Solvent Atoms	205
Heterogen Atoms	63

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
CNS	refinement
CCP4	data scaling
CNS	phasing

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.