5VQX

Crystal Structure of HIV-1 Reverse Transcriptase (Y181C) Variant in Complex with 2-chloro-N-(6-cyano-3-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)phenoxy)-4-methylnaphthalen-1-yl)-N-methylacetamide (JLJ686), a Non-nucleoside Inhibitor


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.8
Temperature 277.0
Details 50 mM imidazole pH 6.8, 16% PEG 8,000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, and 5 mM spermine

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 162.3 α = 90
b = 73.53 β = 99.3
c = 108.67 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2017-02-09
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-E 0.979 APS 24-ID-E

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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
2.4 43.2 99.8 0.048 -- -- 3.708 -- 49576 -- -3.0 48.68
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.4 2.46 99.9 0.511 -- 2.63 3.792 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
FOURIER SYNTHESIS 2.4 43.202 -- 1.35 -- 49571 2000 99.8 -- 0.2273 0.2258 0.2621 Random selection
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.4 2.46 -- 143 3391 0.3017 0.3596 0.0 100.0
X Ray Diffraction 2.46 2.5265 -- 142 3395 0.2915 0.3124 0.0 100.0
X Ray Diffraction 2.5265 2.6009 -- 142 3354 0.2771 0.3488 0.0 100.0
X Ray Diffraction 2.6009 2.6848 -- 141 3386 0.2748 0.3122 0.0 100.0
X Ray Diffraction 2.6848 2.7807 -- 142 3386 0.2676 0.3562 0.0 100.0
X Ray Diffraction 2.7807 2.892 -- 142 3367 0.2685 0.3305 0.0 100.0
X Ray Diffraction 2.892 3.0236 -- 142 3374 0.2747 0.3379 0.0 100.0
X Ray Diffraction 3.0236 3.183 -- 144 3429 0.2672 0.3285 0.0 100.0
X Ray Diffraction 3.183 3.3824 -- 142 3368 0.2534 0.2749 0.0 100.0
X Ray Diffraction 3.3824 3.6434 -- 143 3395 0.2453 0.2818 0.0 100.0
X Ray Diffraction 3.6434 4.0098 -- 142 3373 0.215 0.2395 0.0 99.0
X Ray Diffraction 4.0098 4.5895 -- 143 3419 0.19 0.2237 0.0 100.0
X Ray Diffraction 4.5895 5.7801 -- 144 3428 0.1949 0.2326 0.0 100.0
X Ray Diffraction 5.7801 43.2092 -- 148 3506 0.1815 0.1957 0.0 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 58.2888
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 9.888
f_chiral_restr 0.042
f_bond_d 0.002
f_angle_d 0.488
f_plane_restr 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7736
Nucleic Acid Atoms 0
Heterogen Atoms 46
Solvent Atoms 151

Software

Software
Software Name Purpose
XSCALE data scaling version: Nov 1, 2016
PHENIX refinement version: 1.10.1_2155
PDB_EXTRACT data extraction version: 3.22
XDS data reduction version: Nov 1, 2016
PHENIX phasing version: 1.10.1_2155