Experiment: 4PGN

CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM DESULFOVIBRIO ALASKENSIS G20 (Dde_0634, TARGET EFI-510120) WITH BOUND INDOLE PYRUVATE

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	298	Protein (68.0 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT), Reservoir (0.2 M di-Ammonium Hydrogen Citrate pH 5.0, 20 %(w/v) PEG 3350), Cryoprotection (80% Reservoir + 20% Ethylene Glycol

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.122	α = 90
b = 144.459	β = 90.33
c = 95.466	γ = 90

Symmetry
Space Group	P 1 21 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)	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	1.8	33.9	99.8	0.111	0.066	7.2	3.8		124994			18.15

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	1.8	1.83	99.9		0.8	0.48	1.7	3.7	6132

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	FOURIER SYNTHESIS	FREE R-VALUE	1.8	29.301	1.34	124826	6275	99.71	0.1589	0.1568	0.1582	0.1959	0.1944	Random Selection	27.28

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	13.63
f_angle_d	1.29
f_chiral_restr	0.075
f_bond_d	0.011
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9509
Nucleic Acid Atoms
Solvent Atoms	1249
Heterogen Atoms	134

Software

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