Experiment: 3TDV

Structure of the GDP complex of wild-type aminoglycoside 2'-phosphotransferase-IIIa

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.2 M lithium nitrate, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.68	α = 89.94
b = 54.65	β = 103.83
c = 77.16	γ = 106.84

Symmetry
Space Group	P 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	CCD	RAYONIX MX-325		2010-04-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97946	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.2	38.5	95	0.074	9.6	2		30490

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.25	94.3		0.335	2.51

Refinement

Statistics
Diffraction ID	Structure Solution 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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	2.2	38.452	1.97	30488	1567	95.19	0.2086	0.2042	0.1991	0.2911	0.2821	random 5%

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]
10.7264	8.758	6.0154	-4.4872	4.3936	-6.2393

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	19.139
f_angle_d	1.182
f_chiral_restr	0.072
f_bond_d	0.009
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4803
Nucleic Acid Atoms
Solvent Atoms	291
Heterogen Atoms	62

Software

Software
Software Name	Purpose
Blu-Ice	data collection
MOLREP	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling