7TAZ | pdb_00007taz

Crystal structure of HIV-1 reverse transcriptase (RT) in complex with VM-1500A, a non-nucleoside RT inhibitor

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.4	277	PEG 8,000, ammonium sulfate, Bis tris propane, ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 163.05	α = 90
b = 73.87	β = 99.96
c = 108.64	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 PILATUS3 6M		2020-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.03321	APS	23-ID-D

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	2.4	48.62	99.9	0.049	0.053	0.02	0.999	19.8	6.8		49968

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	2.4	2.48	100		0.769	0.831	0.313	0.876		7

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4G1Q	2.4	48.62	47489	2478	99.92	0.2239	0.2233	0.23	0.2362	0.24	RANDOM	88.277

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]
-2.54		-1.81	-0.73		3.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.528
r_dihedral_angle_3_deg	17.056
r_dihedral_angle_4_deg	14.7
r_dihedral_angle_1_deg	7.662
r_angle_other_deg	2.245
r_angle_refined_deg	1.532
r_chiral_restr	0.067
r_bond_other_d	0.034
r_gen_planes_other	0.009
r_bond_refined_d	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.528
r_dihedral_angle_3_deg	17.056
r_dihedral_angle_4_deg	14.7
r_dihedral_angle_1_deg	7.662
r_angle_other_deg	2.245
r_angle_refined_deg	1.532
r_chiral_restr	0.067
r_bond_other_d	0.034
r_gen_planes_other	0.009
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7955
Nucleic Acid Atoms
Solvent Atoms	276
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	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 R01GM157729.