6AMO

STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE (RT) TERNARY COMPLEX WITH A DOUBLE STRANDED DNA AND AN INCOMING D4TTP AT PH 7.0


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9.5
Temperature 277.0
Details PEG 8000, NaCl, CHES (N-Cyclohexyl-2-aminoethanesulfonic acid), TRIS (tris(hydroxymethyl)aminomethane), MgCl2, d4T triphosphate

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 90.02 α = 90
b = 132.67 β = 98.4
c = 139.39 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 270 100White beam collimating mirror, horizontally focusing monochromator using single bent triangular Si(111) crystal, vertically focusing Rh-coated Si mirror 2010-07-10
Diffraction Radiation
Monochromator Protocol
SI (111) SILICON CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CHESS BEAMLINE F1 0.9177 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
2.5 50 99.2 0.077 -- 21.47 6.4 -- 111018 -- -1.0 56.66
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)
2.5 2.59 97.9 0.722 -- 1.9 5.0 --

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 2.497 43.518 -- 1.38 -- 110980 1970 98.79 -- 0.1814 0.1808 0.2173 --
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 2.4967 2.5591 -- 125 7201 0.2676 0.2809 0.0 92.0
X Ray Diffraction 2.5591 2.6283 -- 141 7764 0.2755 0.3472 0.0 99.0
X Ray Diffraction 2.6283 2.7056 -- 139 7761 0.263 0.3435 0.0 99.0
X Ray Diffraction 2.7056 2.7929 -- 141 7782 0.2547 0.3024 0.0 99.0
X Ray Diffraction 2.7929 2.8927 -- 141 7780 0.2303 0.2566 0.0 99.0
X Ray Diffraction 2.8927 3.0085 -- 142 7837 0.2152 0.252 0.0 99.0
X Ray Diffraction 3.0085 3.1454 -- 140 7807 0.215 0.2443 0.0 100.0
X Ray Diffraction 3.1454 3.3112 -- 143 7842 0.2058 0.2231 0.0 100.0
X Ray Diffraction 3.3112 3.5186 -- 142 7874 0.1845 0.249 0.0 100.0
X Ray Diffraction 3.5186 3.7901 -- 144 7893 0.1744 0.2073 0.0 100.0
X Ray Diffraction 3.7901 4.1712 -- 142 7858 0.157 0.1899 0.0 100.0
X Ray Diffraction 4.1712 4.7741 -- 143 7919 0.1446 0.1761 0.0 100.0
X Ray Diffraction 4.7741 6.0124 -- 143 7935 0.159 0.2042 0.0 100.0
X Ray Diffraction 6.0124 43.5251 -- 144 7757 0.1612 0.1882 0.0 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 93.9048
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_bond_d 0.005
f_angle_d 0.439
f_dihedral_angle_d 13.706
f_chiral_restr 0.039
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 15778
Nucleic Acid Atoms 1716
Heterogen Atoms 138
Solvent Atoms 653

Software

Software
Software Name Purpose
HKL-2000 data reduction
HKL-2000 data scaling
PHASER phasing version: 2.5.6
PHENIX refinement version: 1.11.1 2575
PDB_EXTRACT data extraction version: 3.22
Coot model building version: 0.8.8