6CTO

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CF2, 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 = 50.78 α = 90
b = 79.17 β = 107.1
c = 55.49 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 944 -- 2015-03-31
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
2.04 20 87.9 0.068 -- -- 3.4 -- 23574 -- -- --
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)
2.04 2.08 44.7 0.438 -- -- 2.4 --

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 2.04 19.792 -- 1.34 -- 23556 1999 87.45 -- 0.1832 0.1788 0.2319 --
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 2.0358 2.0866 -- 68 731 0.2253 0.3288 0.0 42.0
X Ray Diffraction 2.0866 2.143 -- 94 1022 0.2403 0.2738 0.0 58.0
X Ray Diffraction 2.143 2.206 -- 111 1197 0.2353 0.3481 0.0 68.0
X Ray Diffraction 2.206 2.2771 -- 127 1364 0.2264 0.253 0.0 79.0
X Ray Diffraction 2.2771 2.3583 -- 144 1553 0.2177 0.2879 0.0 88.0
X Ray Diffraction 2.3583 2.4526 -- 153 1657 0.227 0.2857 0.0 95.0
X Ray Diffraction 2.4526 2.564 -- 159 1716 0.2175 0.2793 0.0 98.0
X Ray Diffraction 2.564 2.6988 -- 161 1736 0.2112 0.3015 0.0 99.0
X Ray Diffraction 2.6988 2.8675 -- 163 1741 0.2064 0.2603 0.0 99.0
X Ray Diffraction 2.8675 3.0881 -- 161 1741 0.1955 0.2454 0.0 99.0
X Ray Diffraction 3.0881 3.3974 -- 163 1762 0.1778 0.2234 0.0 99.0
X Ray Diffraction 3.3974 3.8858 -- 164 1765 0.1588 0.2087 0.0 100.0
X Ray Diffraction 3.8858 4.8836 -- 164 1770 0.1375 0.1864 0.0 100.0
X Ray Diffraction 4.8836 19.7929 -- 167 1802 0.1487 0.1893 0.0 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.775
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.918
f_bond_d 0.008
f_dihedral_angle_d 18.971
f_chiral_restr 0.048
f_plane_restr 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2612
Nucleic Acid Atoms 630
Heterogen Atoms 37
Solvent Atoms 293

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