3HMQ

1.9 Angstrom resolution crystal structure of a NAD synthetase (nadE) from Salmonella typhimurium LT2 in complex with NAD(+)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	295	protein in 300mM NaCl, 10mM Hepes Na pH 7.5, 0.5mM TCEP was mixed at 1:1 v/v ratio with NH4Sulphat 2M, Bis-Tris 0.1m pH 5.5, 10mm NAD-magic solution, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.97	58.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.82	α = 90
b = 91.82	β = 90
c = 75.05	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	MARMOSAIC 300 mm CCD	Be Lenses/Diamond Laue Mono	2009-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.979	APS	21-ID-G

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	1.9	29.06	99.7	13.7	10.1	29311	29311		-3	29.9

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	1.9	1.93	99.9		0.504	2.8	9.4	1350

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.9	29.06	27647	27647	1477	99.74	0.14611	0.14404	0.1866	RANDOM	19.529

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]
-0.4	-0.2		-0.4		0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.611
r_dihedral_angle_4_deg	14.194
r_dihedral_angle_3_deg	9.838
r_dihedral_angle_1_deg	3.336
r_scangle_it	3.056
r_scbond_it	1.911
r_angle_refined_deg	1.374
r_mcangle_it	1.22
r_angle_other_deg	0.918
r_mcbond_it	0.698

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.611
r_dihedral_angle_4_deg	14.194
r_dihedral_angle_3_deg	9.838
r_dihedral_angle_1_deg	3.336
r_scangle_it	3.056
r_scbond_it	1.911
r_angle_refined_deg	1.374
r_mcangle_it	1.22
r_angle_other_deg	0.918
r_mcbond_it	0.698
r_mcbond_other	0.196
r_chiral_restr	0.091
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2049
Nucleic Acid Atoms
Solvent Atoms	432
Heterogen Atoms	84

Software

Software
Software Name	Purpose
Blu-Ice	data collection
REFMAC	refinement
XSCALE	data scaling
XDS	data reduction
XDS	data scaling
Structure	phasing
SHELXD	phasing
SHELXE	model building
Bp3	phasing
SOLOMON	phasing
ARP	model building
WARP	model building

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.