6CR9

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CFCL, beta, gamma dATP 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 = 50.75 α = 90
b = 79.47 β = 107.61
c = 55.65 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 -- 2016-03-14
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
1.96 50 99.5 0.08 -- -- 3.6 -- 30271 -- -- --
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)
1.96 1.99 94.1 0.43 -- -- 2.5 --

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
-- 1.96 23.892 -- 1.34 -- 30120 1993 98.85 -- 0.1825 0.1797 0.2237 --
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 1.9556 2.0045 -- 128 1808 0.231 0.2663 0.0 91.0
X Ray Diffraction 2.0045 2.0586 -- 144 2035 0.2143 0.2479 0.0 100.0
X Ray Diffraction 2.0586 2.1192 -- 142 2008 0.1913 0.2323 0.0 100.0
X Ray Diffraction 2.1192 2.1875 -- 143 2022 0.1935 0.2432 0.0 100.0
X Ray Diffraction 2.1875 2.2657 -- 144 2027 0.2011 0.2541 0.0 100.0
X Ray Diffraction 2.2657 2.3563 -- 143 2019 0.203 0.2813 0.0 100.0
X Ray Diffraction 2.3563 2.4634 -- 143 2020 0.2057 0.2334 0.0 100.0
X Ray Diffraction 2.4634 2.5932 -- 144 2032 0.2117 0.2466 0.0 100.0
X Ray Diffraction 2.5932 2.7554 -- 144 2033 0.2183 0.271 0.0 99.0
X Ray Diffraction 2.7554 2.9678 -- 141 1987 0.221 0.2472 0.0 97.0
X Ray Diffraction 2.9678 3.2658 -- 142 2000 0.2067 0.259 0.0 99.0
X Ray Diffraction 3.2658 3.7368 -- 144 2044 0.1515 0.1909 0.0 100.0
X Ray Diffraction 3.7368 4.7021 -- 144 2023 0.1396 0.1812 0.0 99.0
X Ray Diffraction 4.7021 23.8941 -- 147 2069 0.1489 0.1941 0.0 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.6465
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 17.042
f_bond_d 0.007
f_plane_restr 0.005
f_chiral_restr 0.081
f_angle_d 0.972
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2614
Nucleic Acid Atoms 629
Heterogen Atoms 37
Solvent Atoms 474

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