4H4O

Crystal Structure of HIV-1 Reverse Transcriptase (RT) in Complex with (E)-3-(3-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)- 4-fluorophenoxy)-5-fluorophenyl)acrylonitrile (JLJ506), A Non-nucleoside inhibitor


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 277.0
Details 20% (w/v) PEG 8000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, 5 mM spermine-HCl, 50 mM HEPES pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 225.45 α = 90
b = 69.57 β = 106.21
c = 104.4 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 77
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 Monochromator 2012-06-13
Diffraction Radiation
Monochromator Protocol
Cryogenically cooled double crystal monochrometer with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror. SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A

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
2.9 41.72 99.9 0.072 0.073 -- 3.8 34778 34778 1.5 1.5 79.02
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)
2.9 2.95 99.9 0.596 0.47 2.6 3.7 1693

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
MOLECULAR REPLACEMENT 2.9 41.722 1.89 1.89 35694 34760 1999 99.75 0.2343 0.2324 0.2324 0.265 Random
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 2.8982 2.9706 2252 138 2252 0.3317 0.364 -- 98.0
X Ray Diffraction 2.9706 3.0509 2339 143 2339 0.3176 0.354 -- 100.0
X Ray Diffraction 3.0509 3.1407 2334 141 2334 0.2984 0.3737 -- 100.0
X Ray Diffraction 3.1407 3.242 2294 140 2294 0.2726 0.3666 -- 100.0
X Ray Diffraction 3.242 3.3578 2342 143 2342 0.2804 0.2848 -- 100.0
X Ray Diffraction 3.3578 3.4922 2354 144 2354 0.2611 0.3116 -- 100.0
X Ray Diffraction 3.4922 3.651 2329 141 2329 0.2636 0.2941 -- 100.0
X Ray Diffraction 3.651 3.8434 2339 144 2339 0.2515 0.2856 -- 100.0
X Ray Diffraction 3.8434 4.084 2338 142 2338 0.231 0.2912 -- 100.0
X Ray Diffraction 4.084 4.399 2339 142 2339 0.206 0.2302 -- 100.0
X Ray Diffraction 4.399 4.8411 2349 144 2349 0.2011 0.2396 -- 100.0
X Ray Diffraction 4.8411 5.5403 2359 145 2359 0.2121 0.262 -- 100.0
X Ray Diffraction 5.5403 6.9749 2393 146 2393 0.2424 0.2629 -- 100.0
X Ray Diffraction 6.9749 41.7264 2400 146 2400 0.2004 0.2094 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 164.087
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.534
f_plane_restr 0.004
f_chiral_restr 0.065
f_angle_d 0.876
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8003
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 49

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
HKL data reduction