4NN3 | pdb_00004nn3

Crystal structure of a TRAP periplasmic solute binding protein from Desulfovibrio salexigens (Desal_2161), Target EFI-510109, with bound orotic acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		STRUCTURE SOLVED INITIALLY IN SAME CRYSTAL FORM SOAKED WITH SODIUM IODIDE AND SAD PHASED

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	298	40.2 mg/mL protein in 10 mM HEPES, pH 7.5, 5 mM DTT, reservoir: MCSG1(H9) (0.1 M Bis-Tris, pH 5.5, 25% w/v PEG3350), cryoprotection: 4:1 50% w/v PEG3350:reservoir, ligand copurified with protein, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.78	30.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.346	α = 90
b = 147.006	β = 90
c = 39.272	γ = 90

Symmetry
Space Group	P 21 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	RAYONIX MX225HE	mirrors	2013-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9793	APS	31-ID

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	1.4	147.006	93.6	0.066	0.066	14.9	5.5	53494	53494			10.45

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	1.4	1.48	84.7		0.6	0.6	1.3	4.4	6914

Refinement

Statistics
Diffraction ID	Structure Solution 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	FOURIER SYNTHESIS	STRUCTURE SOLVED INITIALLY IN SAME CRYSTAL FORM SOAKED WITH SODIUM IODIDE AND SAD PHASED	1.4	30.728	53419	53419	2726	93.22	0.1547	0.1547	0.1529	0.16	0.1886	0.19	RANDOM	16.6572

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.913
f_angle_d	1.232
f_chiral_restr	0.061
f_bond_d	0.009
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2451
Nucleic Acid Atoms
Solvent Atoms	434
Heterogen Atoms	22

Software

Software
Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
PHENIX	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.