2PKN

Crystal structure of M tuberculosis Adenosine Kinase complexed with AMP-PCP (non-hydrolyzable ATP analog)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PKF	apo MTB ADK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	290	20% PEG 8000, 100 mM sodium cacodylate pH 6.5, and 200 mM magnesium acetate tetrahydrate , VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.05	α = 90
b = 75.184	β = 109.8
c = 52.38	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	120	IMAGE PLATE	RIGAKU RAXIS IV		2006-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	OTHER	1.5412

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	1.9	57.54	99.87	0.05			25991	25991

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	apo MTB ADK	1.9	57.54	25991	1379	99.87	0.2095	0.20686	0.25781	RANDOM	34.41

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]
-1.68		-1.11	1.04		-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.088
r_dihedral_angle_4_deg	20.99
r_dihedral_angle_3_deg	13.871
r_dihedral_angle_1_deg	6.218
r_scangle_it	6.024
r_scbond_it	4.389
r_mcangle_it	3.367
r_mcbond_it	2.486
r_angle_refined_deg	1.275
r_symmetry_hbond_refined	0.377

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.088
r_dihedral_angle_4_deg	20.99
r_dihedral_angle_3_deg	13.871
r_dihedral_angle_1_deg	6.218
r_scangle_it	6.024
r_scbond_it	4.389
r_mcangle_it	3.367
r_mcbond_it	2.486
r_angle_refined_deg	1.275
r_symmetry_hbond_refined	0.377
r_nbtor_refined	0.293
r_symmetry_vdw_refined	0.25
r_nbd_refined	0.185
r_xyhbond_nbd_refined	0.156
r_chiral_restr	0.088
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2400
Nucleic Acid Atoms
Solvent Atoms	275
Heterogen Atoms	31

Software

Software
Software Name	Purpose
REFMAC	refinement

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.