3NCY | pdb_00003ncy

X-ray crystal structure of an arginine agmatine antiporter (AdiC) in complex with a Fab fragment

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	30-35% PEG 400, 100-200mM CaCl2, 100mM Glycine pH 9-9.5, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.22	70.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.661	α = 81.96
b = 104.149	β = 75.93
c = 154.025	γ = 73.73

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	78	CCD	MARMOSAIC 300 mm CCD		2008-01-01		MAD
2	1	x-ray	78	CCD	ADSC QUANTUM 315		2008-10-29
3	1	x-ray	78

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.97942	APS	23-ID-B
2	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.0809	ALS	8.2.2
3	SYNCHROTRON	NSLS BEAMLINE X29A	1.006	NSLS	X29A

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	2.99	50	98.2	0.086	11.4	3.7		90050

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.99	3.04	94.1			3

Refinement

Statistics
Diffraction ID	Structure Solution 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)	Mean Isotropic B
X-RAY DIFFRACTION		3.2	33.227	1.96	72994	3611	96.37	0.2831	0.2816	0.2748	0.3118	0.3032

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]
-31.2028	-3.0605	-7.5455	-38.0709	-2.8742	-46.0303

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.349
f_angle_d	0.883
f_chiral_restr	0.051
f_plane_restr	0.005
f_bond_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18693
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
PDB_EXTRACT	data extraction
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.