8C8J

Long Interspersed Nuclear Element 1 (LINE-1) reverse transcriptase ternary complex with hybrid duplex and dTTP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	293	PEG8000, sodium citrate, 1,4 dioxane, ethylene glycol, dimethyl sulphoxide
6	VAPOR DIFFUSION	5.6	293	PEG8000, sodium citrate, 1,4 dioxane, ethylene glycol, dimethyl sulphoxide
5	VAPOR DIFFUSION	5.6	293	PEG8000, sodium citrate, 1,4 dioxane, ethylene glycol, dimethyl sulphoxide
4	VAPOR DIFFUSION	5.6	293	PEG8000, sodium citrate, 1,4 dioxane, ethylene glycol, dimethyl sulphoxide
3	VAPOR DIFFUSION	5.6	293	PEG8000, sodium citrate, 1,4 dioxane, ethylene glycol, dimethyl sulphoxide
2	VAPOR DIFFUSION	5.6	293	PEG8000, sodium citrate, 1,4 dioxane, ethylene glycol, dimethyl sulphoxide

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.349	α = 90
b = 84.528	β = 91.48
c = 107.938	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	100	PIXEL	DECTRIS EIGER2 XE 16M		2022-08-05	M	SINGLE WAVELENGTH
6	6	x-ray	100	PIXEL	DECTRIS EIGER2 XE 16M		2022-08-06	M	SINGLE WAVELENGTH
5	5	x-ray	100	PIXEL	DECTRIS EIGER2 XE 16M		2022-08-06	M	SINGLE WAVELENGTH
4	4	x-ray	100	PIXEL	DECTRIS EIGER2 XE 16M		2022-08-06	M	SINGLE WAVELENGTH
3	3	x-ray	100	PIXEL	DECTRIS EIGER2 XE 16M		2022-08-06	M	SINGLE WAVELENGTH
2	2	x-ray	100	PIXEL	DECTRIS EIGER2 XE 16M		2022-08-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03
6	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03
5	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03
4	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03
3	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03
2	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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
1,2,3,4,5,6	2.1	59.66	100	0.018	1	18.7	41.2	62734	62715			49.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2,3,4,5,6	2.1	2.15	100		0.427	0.892	1.9	42.1

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.1	59.66	62715	3001	100	0.2093	0.2079	0.238	RANDOM	61.79

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]
-22.1967		-9.7979	6.9248		15.2719

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	17.16
t_omega_torsion	3.1
t_angle_deg	0.89
t_bond_d	0.008
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5573
Nucleic Acid Atoms	439
Solvent Atoms	219
Heterogen Atoms	128

Software

Software
Software Name	Purpose
BUSTER	refinement
DIALS	data reduction
Aimless	data scaling
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.