1XQE

The mechanism of ammonia transport based on the crystal structure of AmtB of E. coli.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XQF	The same structure in the absence of ammonium

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	298	PEG 550, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.9	68.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.632	α = 90
b = 116.632	β = 90
c = 130.543	γ = 120

Symmetry
Space Group	H 3

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	MARRESEARCH		2004-05-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.9797	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	2.1	79.06	99.7	0.073	13.6	5.8		38583		-3	44.4

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	2.1	2.15	99.9		0.7	2.5	5.7	2677

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	The same structure in the absence of ammonium	2.1	60	36648	36648	1935	99.72	0.16051	0.16051	0.15912	0.18603	RANDOM	42.765

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]
1.58	0.79		1.58		-2.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.451
r_dihedral_angle_4_deg	25.424
r_dihedral_angle_3_deg	13.518
r_scangle_it	6.173
r_dihedral_angle_1_deg	5.267
r_scbond_it	4.726
r_mcangle_it	3.147
r_mcbond_it	2.205
r_angle_refined_deg	1.236
r_nbtor_refined	0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.451
r_dihedral_angle_4_deg	25.424
r_dihedral_angle_3_deg	13.518
r_scangle_it	6.173
r_dihedral_angle_1_deg	5.267
r_scbond_it	4.726
r_mcangle_it	3.147
r_mcbond_it	2.205
r_angle_refined_deg	1.236
r_nbtor_refined	0.307
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.187
r_symmetry_hbond_refined	0.128
r_xyhbond_nbd_refined	0.112
r_chiral_restr	0.085
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2660
Nucleic Acid Atoms
Solvent Atoms	93
Heterogen Atoms	19

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling
AMoRE	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.