4P9K | pdb_00004p9k

CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM VERMINEPHROBACTER EISENIAE EF01-2 (Veis_3954, TARGET EFI-510324) A NEPHRIDIAL SYMBIONT OF THE EARTHWORM EISENIA FOETIDA, BOUND TO D-ERYTHRONATE WITH RESIDUAL DENSITY SUGGESTIVE OF SUPERPOSITION WITH COPURIFIED ALTERNATIVE LIGAND.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	Protein (42.92 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 1 mM D-Erythronate); Reservoir ( 0.1 M Tris pH 8.5 2.4 M di-Ammonium Phosphate ); Cryoprotection (Reservoir + 20% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.29	α = 90
b = 76.29	β = 90
c = 110.813	γ = 120

Symmetry
Space Group	P 32 2 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	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)	CC (Half)	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	110.81	100	0.127	0.032	0.999	16	16.6		142034			14.22

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.42	100		2.287	0.579	0.729	1.7	16.4	3613

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	1.4	26.535	1.34	142034	7193	99.93	0.1489	0.1479	0.16	0.168	0.18	Random Selection	19.69

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	13.354
f_angle_d	1.202
f_chiral_restr	0.073
f_bond_d	0.012
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2326
Nucleic Acid Atoms
Solvent Atoms	475
Heterogen Atoms	9

Software

Software
Software Name	Purpose
MOSFLM	data reduction
PDB_EXTRACT	data extraction
PHENIX	refinement
Aimless	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.