9MH3 | pdb_00009mh3

Structure of N-3 aminoglycoside acetyltransferase XI (AAC(3)-XI) in complex with acetyl coenzyme A

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9MGT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294.15	0.1M Sodium acetate pH 4.6, 10-45% (v/v) 2-methyl-2,4-pentanediol, 0-20% (v/v) PEG 400

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.422	α = 90
b = 99.512	β = 106.4
c = 39.29	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	Bruker PHOTON II		2021-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	LIQUID ANODE	BRUKER METALJET	1.3418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	1.38	28.51	99.89	0.999	15.96	10.9		53467

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.38	1.429			0.824

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation 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	MOLECULAR REPLACEMENT	FREE R-VALUE	1.38	28.51	1.36	53467	2365	99.58	0.1594	0.1586	0.1589	0.1956	0.1958

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	26.267
f_angle_d	1.42
f_chiral_restr	0.091
f_bond_d	0.013
f_plane_restr	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2256
Nucleic Acid Atoms
Solvent Atoms	351
Heterogen Atoms	122

Software

Software
Software Name	Purpose
PHENIX	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling
PHASER	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 R01GM157729.