3I6V

Crystal structure of a periplasmic His/Glu/Gln/Arg/opine family-binding protein from Silicibacter pomeroyi in complex with lysine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.6	294	100mM sodium acetate pH 4.6, 25% PEG 6K, vapor diffusion, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3.57	65.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.931	α = 90
b = 70.931	β = 90
c = 141.359	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	MARMOSAIC 225 mm CCD		2009-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	31.699	99.9	0.111	0.111	17.8	17.6	25236	25211			26.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.11	99.8		0.464	0.464	6.4	17.1	3592

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2	20	25156	25131	1270	99.9	0.2	0.198	0.224	RANDOM	28.385

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]
0.28			0.28		-0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.883
r_dihedral_angle_4_deg	17.423
r_dihedral_angle_3_deg	12.066
r_dihedral_angle_1_deg	5.566
r_scangle_it	4.028
r_scbond_it	2.57
r_mcangle_it	1.614
r_angle_refined_deg	1.425
r_mcbond_it	0.878
r_chiral_restr	0.105

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.883
r_dihedral_angle_4_deg	17.423
r_dihedral_angle_3_deg	12.066
r_dihedral_angle_1_deg	5.566
r_scangle_it	4.028
r_scbond_it	2.57
r_mcangle_it	1.614
r_angle_refined_deg	1.425
r_mcbond_it	0.878
r_chiral_restr	0.105
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1632
Nucleic Acid Atoms
Solvent Atoms	77
Heterogen Atoms	17

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.