4LSN

Crystal Structure of HIV-1 Reverse Transcriptase in Complex with (E)-3-(3-bromo-5-(4-chloro-2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)phenoxy)phenyl)acrylonitrile (JLJ518), 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 15% (w/v) PEG 8000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, 5 mM spermine, and 50 mM citric acid pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 222.82 α = 90
b = 68.59 β = 107.41
c = 103.54 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 2012-10-03
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
2.99 50 97.0 0.078 0.111 -- 3.7 29672 29672 1.5 1.5 93.94
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)
2.99 3.04 99.1 0.488 -- -- 3.8 1479

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 3.1 36.142 1.36 1.36 26498 26498 1788 96.63 0.2563 0.253 0.253 0.3008 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 3.1001 3.1839 1918 139 1918 0.3101 0.3802 -- 99.0
X Ray Diffraction 3.1839 3.2775 1944 142 1944 0.3116 0.3834 -- 99.0
X Ray Diffraction 3.2775 3.3832 1917 138 1917 0.3186 0.3658 -- 99.0
X Ray Diffraction 3.3832 3.504 1912 138 1912 0.3461 0.4589 -- 99.0
X Ray Diffraction 3.504 3.6442 1963 142 1963 0.2985 0.3606 -- 99.0
X Ray Diffraction 3.6442 3.8099 1930 139 1930 0.288 0.3662 -- 99.0
X Ray Diffraction 3.8099 4.0105 1932 140 1932 0.2788 0.3346 -- 98.0
X Ray Diffraction 4.0105 4.2614 1915 139 1915 0.2313 0.2878 -- 99.0
X Ray Diffraction 4.2614 4.5899 1926 139 1926 0.2141 0.2392 -- 98.0
X Ray Diffraction 4.5899 5.0506 1890 136 1890 0.2007 0.2518 -- 96.0
X Ray Diffraction 5.0506 5.7789 1936 141 1936 0.2304 0.2874 -- 98.0
X Ray Diffraction 5.7789 7.2711 1931 140 1931 0.2634 0.2926 -- 97.0
X Ray Diffraction 7.2711 36.1442 1596 115 1596 0.2367 0.2617 -- 78.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 95.0969
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.003
f_plane_restr 0.003
f_angle_d 0.868
f_chiral_restr 0.069
f_dihedral_angle_d 14.43
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7893
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 15

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
PHENIX refinement version: 1.8.2_1309
PDB_EXTRACT data extraction version: 3.11
CBASS data collection
HKL-2000 data reduction
HKL-2000 data scaling