4F4H | pdb_00004f4h

Crystal structure of a Glutamine dependent NAD+ synthetase from Burkholderia thailandensis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3N05

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	290	Internal tracking number 232316c5. Morpheus well C5, 10% w/v PEG20K, 20% PEG MME 550, 0.03M NPS (Sodium nitrate, disodium hydrogen phosphate, ammonium sulfate ), 0.1M MOPS / HEPES-Na pH 7.5 ButhA.18002.a.A1.PS01197 20.0mg/ml., vapor diffusion, sitting drop, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.09	α = 90
b = 73.08	β = 102.76
c = 116.89	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 315	mirrors Rh/Pt coated Si	2012-04-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.033200	ALS	5.0.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.75	49.3	99.8	0.059	18.48	5.74	119513	119307		-3	28.063

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	1.75	1.8	99.9		0.518	3.4

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 (All)	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	THROUGHOUT	3N05	1.75	49.3	119513	119282	5975	99.86	0.154	0.154	0.153	0.16	0.18	0.19	RANDOM	23.246

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]
-0.35		0.21	1.34		-0.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.524
r_dihedral_angle_4_deg	17.693
r_dihedral_angle_3_deg	12.238
r_dihedral_angle_1_deg	5.856
r_angle_refined_deg	1.434
r_angle_other_deg	0.926
r_chiral_restr	0.087
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.524
r_dihedral_angle_4_deg	17.693
r_dihedral_angle_3_deg	12.238
r_dihedral_angle_1_deg	5.856
r_angle_refined_deg	1.434
r_angle_other_deg	0.926
r_chiral_restr	0.087
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8013
Nucleic Acid Atoms
Solvent Atoms	749
Heterogen Atoms	26

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
BOS	data collection
XDS	data reduction

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.