6HAK

Crystal structure of HIV-1 reverse transcriptase (RT) in complex with a double stranded RNA represents the RT transcription initiation complex prior to nucleotide incorporation


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 277.0
Details PEG 8000, AMMONIUM SULFATE, MGCL2, GLYCEROL, SUCROSE

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 175.24 α = 90
b = 175.24 β = 90
c = 225.8 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 S 6M -- 2014-03-28
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CHESS BEAMLINE F1 0.9179 CHESS F1

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
3.95 87.62 99.9 0.236 -- -- 10.8 -- 31549 -- -- 159.27
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)
3.95 4.16 100.0 2.446 -- 0.9 10.1 --

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 3.95 87.62 -- 1.33 -- 31441 1504 99.7 -- 0.296 0.293 0.329 --
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 3.9501 4.0776 -- 137 2691 0.4208 0.4338 -- 100.0
X Ray Diffraction 4.0776 4.2233 -- 125 2667 0.4105 0.3983 -- 100.0
X Ray Diffraction 4.2233 4.3924 -- 137 2683 0.3891 0.3951 -- 100.0
X Ray Diffraction 4.3924 4.5923 -- 125 2683 0.3708 0.4353 -- 100.0
X Ray Diffraction 4.5923 4.8344 -- 114 2703 0.3536 0.4247 -- 100.0
X Ray Diffraction 4.8344 5.1372 -- 142 2698 0.3062 0.3886 -- 100.0
X Ray Diffraction 5.1372 5.5338 -- 148 2686 0.3024 0.3446 -- 100.0
X Ray Diffraction 5.5338 6.0906 -- 137 2735 0.311 0.3806 -- 100.0
X Ray Diffraction 6.0906 6.9716 -- 147 2735 0.2864 0.3565 -- 100.0
X Ray Diffraction 6.9716 8.7822 -- 146 2775 0.2587 0.2972 -- 100.0
X Ray Diffraction 8.7822 87.6415 -- 146 2881 0.2391 0.2624 -- 98.0
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.196
f_angle_d 0.987
f_chiral_restr 0.055
f_bond_d 0.006
f_plane_restr 0.007
Coordinate Error
Parameter Value
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 15644
Nucleic Acid Atoms 1582
Heterogen Atoms 24
Solvent Atoms 1

Software

Software
Software Name Purpose
PHENIX refinement version: (1.12_2829: ???)
MOSFLM data reduction
Aimless data scaling
PHASER phasing