Experiment: 9MGU

Structure of aminoglycoside acetyltransferase AAC(3)-Ia in complex with CoA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Used model from deposition D_1000289484

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295.15	10 mg/mL AAC(3)-Ia with a 10x molar excess of gentamicin and CoASH in 0.1 M Tris Ph 8.5, 0.05 M MgCl2, 20% EtOH, 35% PEG 400.

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.459	α = 90
b = 57.459	β = 90
c = 123.383	γ = 90

Symmetry
Space Group	P 43 21 2

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	DECTRIS EIGER X 9M		2023-02-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.9537	CLSI	08ID-1

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	2.34	28.9	92.84	0.99	7.22	8.4		8695			30.39

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	2.34	2.67			0.765	1.98

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	FOURIER SYNTHESIS	THROUGHOUT	2.34	28.9	1.34	8665	446	92.84	0.2142	0.2117	0.2114	0.2584	0.2589	36.43

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	11.5234
f_angle_d	1.423
f_chiral_restr	0.0632
f_bond_d	0.0124
f_plane_restr	0.0109

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1126
Nucleic Acid Atoms
Solvent Atoms	29
Heterogen Atoms	48

Software

Software
Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
Coot	model building
PHASER	phasing