3C1J

Substrate binding, deprotonation and selectivity at the periplasmic entrance of the E. coli ammonia channel AmtB

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	298	26% PEG 550, 0.1M sodium acetate, 0.2M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.35	63.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.23	α = 90
b = 110.23	β = 90
c = 84.642	γ = 120

Symmetry
Space Group	P 63

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		2006-05-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.9998	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	20	97.5	0.05	17.74			38571		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.1	99.7		0.47	3.44

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB Entry 1XQF	2	15	36605	1936	97.68	0.18285	0.18285	0.18147	0.20974	RANDOM	27.21

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]
1.04	0.52		1.04		-1.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.468
r_dihedral_angle_3_deg	12.621
r_dihedral_angle_4_deg	10.505
r_scangle_it	6.421
r_scbond_it	5.074
r_dihedral_angle_1_deg	4.744
r_mcangle_it	3.043
r_mcbond_it	2.304
r_angle_refined_deg	0.999
r_nbtor_refined	0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.468
r_dihedral_angle_3_deg	12.621
r_dihedral_angle_4_deg	10.505
r_scangle_it	6.421
r_scbond_it	5.074
r_dihedral_angle_1_deg	4.744
r_mcangle_it	3.043
r_mcbond_it	2.304
r_angle_refined_deg	0.999
r_nbtor_refined	0.3
r_nbd_refined	0.187
r_symmetry_vdw_refined	0.149
r_symmetry_hbond_refined	0.139
r_xyhbond_nbd_refined	0.098
r_chiral_restr	0.072
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2636
Nucleic Acid Atoms
Solvent Atoms	120
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

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.