4PFB | pdb_00004pfb

Crystal structure of a TRAP periplasmic solute binding protein from Fusobacterium nucleatun (FN1258, TARGET EFI-510120) with bound SN-glycerol-3-phosphate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4N6K	PDB entry 4N6K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	Protein (70.0 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM Glycerol 3-phosphate); Reservoir (0.2 M Zinc Acetate, 0.1 M Imidazole pH 6.5, 10 %(w/v) PEG 8000); Cryoprotection (80% Reservoir + 20% Glycerol

Crystal Properties
Matthews coefficient	Solvent content
3.25	62.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.574	α = 90
b = 113.574	β = 90
c = 79.937	γ = 90

Symmetry
Space Group	P 43 2 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	2013-12-06	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 Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	2.7	113.574	99.9	0.166	0.173	0.05	10.4	11.8	14902	14902			52.93

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.85	100		0.854	0.854	0.254	0.9	12	2135

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation 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	FREE R-VALUE	PDB entry 4N6K	2.7	40.154	1.36	14870	753	99.77	0.1663	0.1644	0.17	0.2037	0.2	Random Selection	40.85

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	15.4
f_angle_d	1.094
f_chiral_restr	0.072
f_bond_d	0.012
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2419
Nucleic Acid Atoms
Solvent Atoms	81
Heterogen Atoms	25

Software

Software
Software Name	Purpose
SCALA	data scaling
PDB_EXTRACT	data extraction
PHENIX	refinement
SCALA	data scaling

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.