6QBV

Structure of the HTLV-2 integrase catalytic core domain in complex with magnesium (dimeric form)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291	100 mM Tris pH 8.5, 14% PEG 8000, 250 mM magnesium chloride

Crystal Properties
Matthews coefficient	Solvent content
3.45	69.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 185.315	α = 90
b = 89.175	β = 102.485
c = 65.53	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	291	PIXEL	DECTRIS PILATUS3 S 6M		2017-10-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.45	58.611	100	0.242	0.342	0.146	0.923	3	3.9		38400

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	2.45	2.55	100		0.383		3.9

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	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6QBV	2.45	58.611	38400	1876	99.914	0.235	0.2326	0.2725	0.05	69.472

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]
5.006		2.061	-4.528		-1.267

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.83
r_dihedral_angle_4_deg	18.495
r_dihedral_angle_3_deg	17.359
r_lrange_it	13.143
r_scangle_it	11.427
r_mcangle_it	9.157
r_scbond_it	8.832
r_dihedral_angle_1_deg	7.074
r_mcbond_it	6.812
r_angle_refined_deg	1.624

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.83
r_dihedral_angle_4_deg	18.495
r_dihedral_angle_3_deg	17.359
r_lrange_it	13.143
r_scangle_it	11.427
r_mcangle_it	9.157
r_scbond_it	8.832
r_dihedral_angle_1_deg	7.074
r_mcbond_it	6.812
r_angle_refined_deg	1.624
r_nbtor_refined	0.312
r_nbd_refined	0.224
r_symmetry_xyhbond_nbd_refined	0.224
r_symmetry_nbd_refined	0.182
r_xyhbond_nbd_refined	0.175
r_chiral_restr	0.127
r_bond_refined_d	0.008
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4640
Nucleic Acid Atoms
Solvent Atoms	100
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building
xia2	data reduction
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 R01GM133198.