6TOQ

Crystal structure of a PP2A B56y/HTLV-1 integrase complex

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	293.15	0.1 M Na/KPO4 pH 6.2, 20-% 1,2-propanediol, 10% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.77	α = 90
b = 58.77	β = 90
c = 321.15	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	277	PIXEL	DECTRIS PILATUS3 6M		2017-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9192	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	3.16	80.29	96.7	0.167	0.167	0.918	3.3	1.4		10041

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.16	3.38	94.4		0.489	0.589	1.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2JAK	3.164	80.29	10041	537	95.912	0.231	0.227	0.2941	57.582

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]
0.25			0.25		-0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.698
r_dihedral_angle_4_deg	25.598
r_dihedral_angle_3_deg	22.322
r_lrange_it	13.179
r_scangle_it	9.878
r_dihedral_angle_1_deg	9.354
r_mcangle_it	8.127
r_scbond_it	6.471
r_mcbond_it	5.316
r_angle_refined_deg	1.655

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.698
r_dihedral_angle_4_deg	25.598
r_dihedral_angle_3_deg	22.322
r_lrange_it	13.179
r_scangle_it	9.878
r_dihedral_angle_1_deg	9.354
r_mcangle_it	8.127
r_scbond_it	6.471
r_mcbond_it	5.316
r_angle_refined_deg	1.655
r_nbtor_refined	0.33
r_symmetry_nbd_refined	0.304
r_nbd_refined	0.282
r_xyhbond_nbd_refined	0.16
r_symmetry_xyhbond_nbd_refined	0.146
r_chiral_restr	0.14
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2674
Nucleic Acid Atoms
Solvent Atoms	46
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building
xia2	data reduction
PHASER	phasing

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.