3C1G

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XQF	PDB Entry 1XQF

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
3.29	62.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.329	α = 90
b = 109.329	β = 90
c = 84.821	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		2007-05-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.9772	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	2.3	20	98.7	0.05	17.2			25706		-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)
	2.3	2.4	97.6		0.48	2.48

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	2.3	15	36372	24136	1300	99.36	0.18788	0.18788	0.18507	0.24203	RANDOM	35.155

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]
2.06	1.03		2.06		-3.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.011
r_dihedral_angle_3_deg	14.592
r_dihedral_angle_4_deg	9.378
r_scangle_it	6.071
r_dihedral_angle_1_deg	5.214
r_scbond_it	5.107
r_mcangle_it	2.975
r_mcbond_it	1.906
r_angle_refined_deg	1.19
r_nbtor_refined	0.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.011
r_dihedral_angle_3_deg	14.592
r_dihedral_angle_4_deg	9.378
r_scangle_it	6.071
r_dihedral_angle_1_deg	5.214
r_scbond_it	5.107
r_mcangle_it	2.975
r_mcbond_it	1.906
r_angle_refined_deg	1.19
r_nbtor_refined	0.315
r_nbd_refined	0.23
r_symmetry_vdw_refined	0.225
r_xyhbond_nbd_refined	0.14
r_symmetry_hbond_refined	0.127
r_chiral_restr	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2648
Nucleic Acid Atoms
Solvent Atoms	87
Heterogen Atoms	14

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 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 R01GM133198.