3DLA | pdb_00003dla

X-ray crystal structure of glutamine-dependent NAD+ synthetase from Mycobacterium tuberculosis bound to NaAD+ and DON

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	293	1.8 M ammonium citrate tribasic dihydrate, 5 % glycerol, pH 7.0, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 178.13	α = 90
b = 178.13	β = 90
c = 215.177	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					M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97949	APS	24-ID-C

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	2.35	29.7	99.3	0.139		11.4	143290	142287	1	1	42.2

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	2.35	2.41	99		0.56		5.3	9636

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.35	29.7	143290	135143	7144	99.4	0.18743	0.18439	0.1866	0.24566	0.246	RANDOM	6.71

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]
-0.05			-0.05		0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.357
r_dihedral_angle_4_deg	18.982
r_dihedral_angle_3_deg	18.929
r_dihedral_angle_1_deg	7.02
r_scangle_it	2.669
r_angle_refined_deg	1.659
r_scbond_it	1.636
r_mcangle_it	0.968
r_mcbond_it	0.582
r_nbtor_refined	0.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.357
r_dihedral_angle_4_deg	18.982
r_dihedral_angle_3_deg	18.929
r_dihedral_angle_1_deg	7.02
r_scangle_it	2.669
r_angle_refined_deg	1.659
r_scbond_it	1.636
r_mcangle_it	0.968
r_mcbond_it	0.582
r_nbtor_refined	0.312
r_symmetry_vdw_refined	0.264
r_nbd_refined	0.238
r_symmetry_hbond_refined	0.212
r_xyhbond_nbd_refined	0.203
r_chiral_restr	0.11
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20221
Nucleic Acid Atoms
Solvent Atoms	1443
Heterogen Atoms	306

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	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.