4DY6

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with 2'-phosphate bis(adenosine)-5'-diphosphate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2I2C	PDB ENTRY 2I2C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.4	291	0.3 M potassium chloride, 50 mM tri-sodium citrate dihydrate, 15-20% w/v PEG400, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.1	α = 90
b = 75.73	β = 90
c = 118.85	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		2006-04-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.933	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.2	63.888	99.1	0.048	0.048	18.6	3.2		14651

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.32	94.5		0.46	0.46	1.6	2.1	1976

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2I2C	2.2	33.55	14823	14651	737	98.84	0.2085	0.2063	0.2504	RANDOM	48.0938

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]
-0.32			0.89		-0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.992
r_dihedral_angle_4_deg	20.062
r_dihedral_angle_3_deg	15.595
r_dihedral_angle_1_deg	6.301
r_scangle_it	1.955
r_mcangle_it	1.594
r_angle_other_deg	1.378
r_angle_refined_deg	1.293
r_scbond_it	1.252
r_mcbond_it	0.878

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.992
r_dihedral_angle_4_deg	20.062
r_dihedral_angle_3_deg	15.595
r_dihedral_angle_1_deg	6.301
r_scangle_it	1.955
r_mcangle_it	1.594
r_angle_other_deg	1.378
r_angle_refined_deg	1.293
r_scbond_it	1.252
r_mcbond_it	0.878
r_mcbond_other	0.108
r_chiral_restr	0.074
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2058
Nucleic Acid Atoms
Solvent Atoms	100
Heterogen Atoms	62

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
AMoRE	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.