3V8P | pdb_00003v8p

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a new di-adenosine inhibitor formed in situ

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	291.15	30 mM sodium bromide, 220 mM potassium citrate, pH 4.8-5.1, glycerol 6%, 15-16% w/v polyethylene glycol 400, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.95	α = 90
b = 75.64	β = 90
c = 118.76	γ = 90

Symmetry
Space Group	I 2 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	ADSC QUANTUM 315r		2009-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	1.03900	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.29	63.76	99.2		4.8		12686

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.29	2.41	100			5.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	Isomorphous replacement	2.2901	33.511	1.38	13133	12686	372	96.59	0.1989	0.1974	0.19	0.2458	0.24

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]
-1.4356			0.0651		1.3705

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.089
f_angle_d	0.934
f_chiral_restr	0.065
f_bond_d	0.004
f_plane_restr	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2066
Nucleic Acid Atoms
Solvent Atoms	113
Heterogen Atoms	58

Software

Software
Software Name	Purpose
ADSC	data collection
PHENIX	refinement
MOSFLM	data reduction
SCALA	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.