4O4G

Crystal Structure of HIV-1 Reverse Transcriptase in complex with 4-((4-(mesitylamino)-1,3,5-triazin-2-yl)amino)benzonitrile (JLJ527), 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 20.0% (w/v) PEG 8000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, 5 mM spermine-HCl, and 50 mM citric acid pH 5.5 or 50 mM HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 163.04 α = 90
b = 73.4 β = 100.06
c = 109.73 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 2013-08-03
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
2.63 50 98.9 0.063 0.065 -- 3.7 -- 38084 -- -3.0 70.95
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)
2.63 2.68 99.9 -- 0.429 -- 3.8 --

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 2.712 43.239 -- 1.36 -- 34310 2000 98.46 -- 0.2395 0.2358 0.2995 --
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 2.7125 2.7803 -- 139 2252 0.304 0.3892 -- 97.0
X Ray Diffraction 2.7803 2.8554 -- 142 2275 0.2672 0.3487 -- 99.0
X Ray Diffraction 2.8554 2.9395 -- 142 2300 0.2627 0.3422 -- 99.0
X Ray Diffraction 2.9395 3.0343 -- 142 2296 0.2675 0.3206 -- 99.0
X Ray Diffraction 3.0343 3.1427 -- 142 2301 0.2533 0.2945 -- 99.0
X Ray Diffraction 3.1427 3.2685 -- 142 2292 0.2462 0.3285 -- 99.0
X Ray Diffraction 3.2685 3.4172 -- 144 2336 0.243 0.3384 -- 99.0
X Ray Diffraction 3.4172 3.5973 -- 142 2295 0.2582 0.3295 -- 99.0
X Ray Diffraction 3.5973 3.8225 -- 143 2317 0.2397 0.3522 -- 99.0
X Ray Diffraction 3.8225 4.1175 -- 145 2329 0.2355 0.3207 -- 99.0
X Ray Diffraction 4.1175 4.5314 -- 145 2334 0.2184 0.3028 -- 99.0
X Ray Diffraction 4.5314 5.1862 -- 144 2343 0.2146 0.2785 -- 99.0
X Ray Diffraction 5.1862 6.5305 -- 146 2356 0.2494 0.2723 -- 99.0
X Ray Diffraction 6.5305 43.2446 -- 142 2284 0.2146 0.2432 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 63.74
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.863
f_chiral_restr 0.059
f_plane_restr 0.004
f_bond_d 0.004
f_dihedral_angle_d 13.616
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8044
Nucleic Acid Atoms 0
Heterogen Atoms 25
Solvent Atoms 35

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHENIX refinement version: 1.8_1069
PDB_EXTRACT data extraction version: 3.14
CBASS data collection
HKL-2000 data reduction
PHASER phasing