6CTV

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CF2, beta, gamma dCTP 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 = 50.67 α = 90
b = 79.25 β = 107.75
c = 55.34 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
PIXEL DECTRIS PILATUS3 X CdTe 1M -- 2017-05-04
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
2.02 50 98.9 0.069 -- -- 3.3 -- 27204 -- -- --
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)
2.02 2.05 86.2 0.398 -- -- 2.1 --

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 2.02 23.616 -- 1.33 -- 26817 1973 97.39 -- 0.1829 0.18 0.2202 --
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 2.016 2.0663 -- 121 1528 0.2577 0.32 0.0 85.0
X Ray Diffraction 2.0663 2.1222 -- 142 1773 0.2014 0.2511 0.0 98.0
X Ray Diffraction 2.1222 2.1846 -- 143 1813 0.1882 0.2362 0.0 100.0
X Ray Diffraction 2.1846 2.255 -- 144 1818 0.1914 0.2547 0.0 100.0
X Ray Diffraction 2.255 2.3356 -- 144 1814 0.1961 0.2609 0.0 100.0
X Ray Diffraction 2.3356 2.429 -- 146 1828 0.2086 0.2637 0.0 100.0
X Ray Diffraction 2.429 2.5394 -- 142 1797 0.2167 0.2859 0.0 99.0
X Ray Diffraction 2.5394 2.6731 -- 144 1786 0.2163 0.2675 0.0 99.0
X Ray Diffraction 2.6731 2.8403 -- 135 1724 0.2431 0.2998 0.0 94.0
X Ray Diffraction 2.8403 3.0592 -- 131 1658 0.2388 0.2632 0.0 91.0
X Ray Diffraction 3.0592 3.3663 -- 144 1817 0.1762 0.2243 0.0 100.0
X Ray Diffraction 3.3663 3.8516 -- 146 1835 0.1514 0.1827 0.0 100.0
X Ray Diffraction 3.8516 4.8457 -- 143 1797 0.1434 0.1764 0.0 98.0
X Ray Diffraction 4.8457 23.618 -- 148 1856 0.1477 0.1662 0.0 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.4264
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.905
f_dihedral_angle_d 18.404
f_chiral_restr 0.049
f_plane_restr 0.005
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2612
Nucleic Acid Atoms 631
Heterogen Atoms 56
Solvent Atoms 388

Software

Software
Software Name Purpose
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX refinement version: 1.10.1_2155
PDB_EXTRACT data extraction version: 3.24
PHENIX phasing