4PFI | pdb_00004pfi

Crystal structure of a tRAP periplasmic solute binding protein from marinobacter aquaeolei VT8 (Maqu_2829, TARGET EFI-510133), apo open structure

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	Protein (55.0 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT); Reservoir (3.5 M Sodium Format pH 7.0); Cryoprotection (80% 7M Sodium Formate + 20% Reservoir)

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.841	α = 90
b = 85.841	β = 90
c = 170.015	γ = 120

Symmetry
Space Group	P 61 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	2014-02-24	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)	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	2.3	100	99.7	0.146	7.1	41.5		17145

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.34	100			41.2	836

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	FREE R-VALUE	2.3024	28.336	1.33	30828	1568	99.25	0.1879	0.1856	0.2	0.2323	0.24	Random Selection	31.63

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	15.211
f_angle_d	1.139
f_chiral_restr	0.07
f_bond_d	0.011
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2374
Nucleic Acid Atoms
Solvent Atoms	144
Heterogen Atoms	1

Software

Software
Software Name	Purpose
PDB_EXTRACT	data extraction
PHENIX	refinement
DENZO	data reduction
SCALEPACK	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.