4P8B | pdb_00004p8b

CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM RALSTONIA EUTROPHA H16 (H16_A1328), TARGET EFI-510189, WITH BOUND (S)-2-hydroxy-2-methyl-3-oxobutanoate ((S)-2-Acetolactate)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	Protein (35.72 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT); Reservoir (0.1 M HEPES pH 7.0, 30 %(v/v) Jeffamine ED-2001 pH 7.0); Cryoprotection (Reservoir, Pause 5 secs in air, prior to vitrification in liquid nitrogen)

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 140.193	α = 90
b = 140.193	β = 90
c = 38.579	γ = 120

Symmetry
Space Group	H 3

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	2014-03-21	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)	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	1.3	40.47	98.8	0.101	0.031	15.9	11.1		68680			11.83

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.32	96.6		0.838	0.275	2.9	10.1	3317

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	1.3	26.494	1.96	137239	6934	98.71	0.1549	0.1539	0.16	0.1742	0.18	Random Selection	19

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	13.127
f_angle_d	1.246
f_chiral_restr	0.07
f_bond_d	0.009
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2428
Nucleic Acid Atoms
Solvent Atoms	417
Heterogen Atoms	11

Software

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

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.