9NLP | pdb_00009nlp

HIV-1 Reverse Transcriptase with New Non-Nucleoside Reverse Transcriptase Inhibitor 12126065

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4G1Q

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	6.7608
f_angle_d	0.6402
f_chiral_restr	0.044
f_plane_restr	0.0057
f_bond_d	0.0036

Sample
HIV-1 reverse transcriptase with novel inhibitor

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	LEICA EM GP
Cryogen Name	ETHANE
Sample Vitrification Details	The cryo-EM grids used for single particle collection were Quantifoil R 2/1 300 gold mesh grids with carbon coating. The grids were glow-discharged f ...	The cryo-EM grids used for single particle collection were Quantifoil R 2/1 300 gold mesh grids with carbon coating. The grids were glow-discharged for 25 s at 25 mA with the chamber pressure set at 0.3 mbar (PELCO easiGlow; Ted Pella). The grids were prepared using the Leica GP2 plunge freezer with its chamber set to 10oC and 95% humidity. Samples of purified HIV-1 RT were diluted to 1mg/mL and 2 molar equivalents of the appropriate compound 12126065 were incubated on a 4oC rotator overnight to combine. A total of 4uL of HIV-1 RT and compound were applied to the backside of the Quantifoil grid and blotted for 4 seconds on the carbon side before plunge frozen in ethane at -181oC.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	175711
Reported Resolution (Å)	3.53
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (4G1Q)
Refinement Space	REAL
Refinement Protocol	AB INITIO MODEL
Refinement Target
Overall B Value	125
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	50

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		6268754

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 R01GM157729.