8U6G

Crystal Structure of HIV-1 Reverse Transcriptase in Complex with 3-(2-(2-(3-acryloyl-2-oxo-2,3-dihydro-1H-benzo[d]imidazol-1-yl)ethoxy)-4-chlorophenoxy)-5-chlorobenzonitrile (JLJ744), a non-nucleoside inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6X4C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	277	50 mM Imidazole pH 6.8, 14% PEG 8000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, and 5 mM spermine

Crystal Properties
Matthews coefficient	Solvent content
3.36	63.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 224.206	α = 90
b = 68.746	β = 107.42
c = 104.123	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 EIGER X 9M		2022-11-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.9201	NSLS-II	17-ID-1

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	2.77	99.3	99.4	0.094	0.111	0.059	0.996	9.8	6.8		38419

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.77	2.823	99.4		2.497	2.923	1.513	0.332

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	2.77	99.3	36413	1927	99.19	0.21542	0.2126	0.26998	RANDOM	101.419

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]
2.37		3.32	-2.94		-1.27

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	19.519
r_long_range_B_other	19.518
r_dihedral_angle_3_deg	19.167
r_scangle_other	16.583
r_mcangle_it	15.785
r_mcangle_other	15.784
r_scbond_it	11.282
r_scbond_other	11.281
r_mcbond_it	10.968
r_mcbond_other	10.966
r_dihedral_angle_2_deg	8.154
r_dihedral_angle_1_deg	7.1
r_angle_refined_deg	1.429
r_angle_other_deg	0.482
r_chiral_restr	0.061
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7438
Nucleic Acid Atoms
Solvent Atoms	10
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing