Experiment: 3SYT

Crystal structure of glutamine-dependent NAD+ synthetase from M. tuberculosis bound to AMP/PPi, NAD+, and glutamate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DLA	PDB ENTRY 3DLA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	8	288	1.2 M ammonium citrate tribasic dihydrate, 5 % glycerol , pH 8.0, EVAPORATION, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 177.755	α = 90
b = 177.755	β = 90
c = 213.059	γ = 90

Symmetry
Space Group	P 41 21 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	MARMOSAIC 325 mm CCD		2009-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.98	SSRL	BL11-1

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	2.65	50	98.6	0.088	20.4	8.2		97718		1

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)
1	2.65	2.74	95.8		0.388	4.1	5.8	9359

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 3DLA	2.6511	49.3	1.34	97557	4871	98.51	0.1571	0.1548	0.1595	0.2	0.2041	RANDOM

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]
-16.5707			-16.5707		33.1415

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.361
f_angle_d	1.561
f_chiral_restr	0.09
f_bond_d	0.015
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20193
Nucleic Acid Atoms
Solvent Atoms	486
Heterogen Atoms	356

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling