6ECL

Crystal Structure of a 1,2,4-Triazole Allosteric RNase H Inhibitor in Complex with HIV Reverse Transcriptase


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 6
Temperature 277.0
Details PEG 3350, SODIUM POTASSIUM PHOSPHATE, BIS TRIS PROPANE

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 163.11 α = 90
b = 73.41 β = 100.43
c = 108.58 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 NOIR-1 -- 2013-08-13
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 4.2.2 1.000 ALS 4.2.2

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
2.38 19.77 97.6 0.035 -- -- 3.7 -- 49173 -- -- 47.23
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)
2.38 2.46 86.7 0.21 -- -- 3.3 --

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 2.385 19.768 -- 1.34 -- 49074 2463 97.29 -- 0.1872 0.1851 0.2289 --
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 2.3849 2.4306 -- 96 2084 0.259 0.2855 0.0 78.0
X Ray Diffraction 2.4306 2.4802 -- 142 2532 0.2419 0.3003 0.0 96.0
X Ray Diffraction 2.4802 2.534 -- 124 2581 0.2148 0.2524 0.0 98.0
X Ray Diffraction 2.534 2.5928 -- 138 2574 0.2146 0.2709 0.0 98.0
X Ray Diffraction 2.5928 2.6575 -- 152 2594 0.2122 0.2714 0.0 98.0
X Ray Diffraction 2.6575 2.7292 -- 147 2621 0.2116 0.2748 0.0 98.0
X Ray Diffraction 2.7292 2.8093 -- 161 2592 0.2242 0.2782 0.0 98.0
X Ray Diffraction 2.8093 2.8997 -- 139 2599 0.218 0.2863 0.0 98.0
X Ray Diffraction 2.8997 3.003 -- 135 2610 0.2135 0.2843 0.0 98.0
X Ray Diffraction 3.003 3.1228 -- 138 2609 0.2245 0.3072 0.0 98.0
X Ray Diffraction 3.1228 3.2643 -- 123 2627 0.219 0.2816 0.0 99.0
X Ray Diffraction 3.2643 3.4355 -- 131 2641 0.2037 0.2286 0.0 99.0
X Ray Diffraction 3.4355 3.6495 -- 132 2626 0.1925 0.211 0.0 99.0
X Ray Diffraction 3.6495 3.9293 -- 142 2622 0.1729 0.2388 0.0 99.0
X Ray Diffraction 3.9293 4.321 -- 124 2657 0.1598 0.2058 0.0 99.0
X Ray Diffraction 4.321 4.9377 -- 162 2639 0.1511 0.1701 0.0 99.0
X Ray Diffraction 4.9377 6.1891 -- 133 2667 0.1734 0.2123 0.0 99.0
X Ray Diffraction 6.1891 19.7685 -- 144 2736 0.1594 0.1969 0.0 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 69.8504
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.004
f_dihedral_angle_d 13.882
f_angle_d 0.6
f_chiral_restr 0.045
f_plane_restr 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7854
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 187

Software

Software
Software Name Purpose
XDS data reduction
Aimless data scaling version: 0.5.25
PHASER phasing version: 2.6.1
PHENIX refinement version: 1.10.1
PDB_EXTRACT data extraction version: 3.24