4PDY

Crystal structure of aminoglycoside phosphotransferase from Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	287	0.5M potassium thiocyanate, 1.0M sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
1.75	29.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.522	α = 90
b = 51.955	β = 90
c = 145.851	γ = 90

Symmetry
Space Group	P 21 21 21

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	ADSC QUANTUM 315r		2012-08-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97935	APS	19-ID

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	1.35	50	99.7	0.067	10.4	6.9	63763	63586		-3

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	1.35	1.36	96.5		0.535		4.5	1533

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.35	29.86	63488	3220	99.56	0.133	0.1309	0.1736	RANDOM	17.878

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]
-0.7			-1.86		2.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.163
r_sphericity_free	31.717
r_dihedral_angle_4_deg	16.445
r_dihedral_angle_3_deg	12.526
r_sphericity_bonded	11.32
r_dihedral_angle_1_deg	5.012
r_rigid_bond_restr	2.437
r_angle_refined_deg	1.29
r_angle_other_deg	0.78
r_chiral_restr	0.083

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.163
r_sphericity_free	31.717
r_dihedral_angle_4_deg	16.445
r_dihedral_angle_3_deg	12.526
r_sphericity_bonded	11.32
r_dihedral_angle_1_deg	5.012
r_rigid_bond_restr	2.437
r_angle_refined_deg	1.29
r_angle_other_deg	0.78
r_chiral_restr	0.083
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2702
Nucleic Acid Atoms
Solvent Atoms	360
Heterogen Atoms	24

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.