6CTL

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCL-R/S isomers, beta, gamma dTTP analogue


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 291.0
Details 16-18% PEG 3350

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.86 α = 90
b = 79.7 β = 107.66
c = 55.12 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 RIGAKU SATURN 92 -- 2014-02-03
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 1.5418 -- --

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 50 96.6 0.11 -- -- 3.3 -- 27487 -- -- --
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)
2.0 2.07 75.7 0.36 -- -- 2.0 --

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 2.0 22.201 -- 1.34 -- 51200 3740 91.23 -- 0.1826 0.1792 0.2253 --
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 1.9953 2.0205 -- 85 865 0.3147 0.3713 0.0 45.0
X Ray Diffraction 2.0205 2.0471 -- 98 1113 0.2913 0.2689 0.0 59.0
X Ray Diffraction 2.0471 2.0751 -- 90 1292 0.2815 0.3007 0.0 68.0
X Ray Diffraction 2.0751 2.1047 -- 115 1416 0.2584 0.3009 0.0 72.0
X Ray Diffraction 2.1047 2.1361 -- 129 1541 0.2477 0.267 0.0 81.0
X Ray Diffraction 2.1361 2.1695 -- 112 1783 0.2361 0.2932 0.0 91.0
X Ray Diffraction 2.1695 2.205 -- 174 1870 0.2248 0.2637 0.0 95.0
X Ray Diffraction 2.205 2.243 -- 140 1793 0.225 0.2833 0.0 96.0
X Ray Diffraction 2.243 2.2838 -- 139 1831 0.2234 0.2334 0.0 96.0
X Ray Diffraction 2.2838 2.3276 -- 150 1881 0.2191 0.2969 0.0 97.0
X Ray Diffraction 2.3276 2.3751 -- 154 1860 0.2122 0.2543 0.0 97.0
X Ray Diffraction 2.3751 2.4267 -- 148 1893 0.2158 0.2511 0.0 97.0
X Ray Diffraction 2.4267 2.4831 -- 138 1872 0.2133 0.2852 0.0 97.0
X Ray Diffraction 2.4831 2.5451 -- 147 1846 0.2202 0.2752 0.0 97.0
X Ray Diffraction 2.5451 2.6138 -- 133 1893 0.2171 0.2556 0.0 97.0
X Ray Diffraction 2.6138 2.6906 -- 163 1830 0.2077 0.2788 0.0 98.0
X Ray Diffraction 2.6906 2.7772 -- 145 1907 0.215 0.3105 0.0 98.0
X Ray Diffraction 2.7772 2.8763 -- 140 1854 0.2177 0.2888 0.0 96.0
X Ray Diffraction 2.8763 2.9912 -- 144 1876 0.2121 0.2943 0.0 97.0
X Ray Diffraction 2.9912 3.127 -- 154 1866 0.2137 0.2737 0.0 98.0
X Ray Diffraction 3.127 3.2914 -- 157 1923 0.1813 0.2336 0.0 100.0
X Ray Diffraction 3.2914 3.4968 -- 144 1918 0.1566 0.1904 0.0 100.0
X Ray Diffraction 3.4968 3.7656 -- 143 1925 0.1505 0.195 0.0 100.0
X Ray Diffraction 3.7656 4.1424 -- 154 1899 0.1383 0.1831 0.0 99.0
X Ray Diffraction 4.1424 4.7367 -- 145 1901 0.1253 0.1748 0.0 98.0
X Ray Diffraction 4.7367 5.9487 -- 151 1909 0.1486 0.162 0.0 99.0
X Ray Diffraction 5.9487 22.2025 -- 148 1903 0.1437 0.1824 0.0 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.5864
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.062
f_dihedral_angle_d 21.561
f_bond_d 0.008
f_chiral_restr 0.043
f_plane_restr 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2608
Nucleic Acid Atoms 630
Heterogen Atoms 35
Solvent Atoms 298

Software

Software
Software Name Purpose
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX refinement version: 1.9_1692
PDB_EXTRACT data extraction version: 3.24
PHENIX phasing