5VQW

Crystal Structure of HIV-1 Reverse Transcriptase (Y181C) Variant in Complex with N-(6-cyano-3-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)phenoxy)-4-methylnaphthalen-1-yl)acrylamide (JLJ685), a Non-nucleoside Inhibitor


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 277.0
Details 50 mM HEPES pH 7.0, 16% PEG 8,000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, and 5 mM spermine

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 162.06 α = 90
b = 73.82 β = 99.61
c = 108.2 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 -- 2017-02-10
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
2.5 43.19 99.7 0.037 -- -- 3.756 -- 43755 -- -3.0 58.24
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)
2.5 2.56 99.9 0.549 -- 2.46 3.808 --

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 2.5 43.193 -- 1.34 -- 43748 2000 99.72 -- 0.2337 0.2326 0.2568 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 2.5 2.5625 -- 142 2970 0.3152 0.3674 0.0 100.0
X Ray Diffraction 2.5625 2.6318 -- 143 2987 0.2955 0.3635 0.0 100.0
X Ray Diffraction 2.6318 2.7093 -- 142 2954 0.292 0.3381 0.0 100.0
X Ray Diffraction 2.7093 2.7967 -- 143 2972 0.2995 0.3189 0.0 100.0
X Ray Diffraction 2.7967 2.8966 -- 140 2938 0.2784 0.3254 0.0 100.0
X Ray Diffraction 2.8966 3.0126 -- 142 2962 0.2764 0.2907 0.0 100.0
X Ray Diffraction 3.0126 3.1496 -- 143 2990 0.2806 0.369 0.0 100.0
X Ray Diffraction 3.1496 3.3156 -- 144 3000 0.274 0.3016 0.0 100.0
X Ray Diffraction 3.3156 3.5233 -- 142 2971 0.2508 0.2815 0.0 100.0
X Ray Diffraction 3.5233 3.7952 -- 141 2945 0.2392 0.2494 0.0 100.0
X Ray Diffraction 3.7952 4.1768 -- 144 2994 0.213 0.2301 0.0 100.0
X Ray Diffraction 4.1768 4.7805 -- 143 2993 0.1996 0.1998 0.0 100.0
X Ray Diffraction 4.7805 6.0204 -- 145 3023 0.2119 0.251 0.0 100.0
X Ray Diffraction 6.0204 43.1996 -- 146 3049 0.1952 0.2112 0.0 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 72.9922
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_bond_d 0.002
f_dihedral_angle_d 9.708
f_angle_d 0.493
f_chiral_restr 0.042
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7730
Nucleic Acid Atoms 0
Heterogen Atoms 41
Solvent Atoms 61

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