6CR8

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCL (R & S isomers), 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 = 50.58 α = 90
b = 78.6 β = 107.14
c = 55.47 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 -- 2015-04-28
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
2.05 20 97.3 0.105 -- -- 3.2 -- 25685 -- -- --
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)
2.05 2.12 81.6 0.5 -- -- 2.2 --

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 2.05 19.282 -- 1.34 -- 25551 1991 96.54 -- 0.195 0.1906 0.2483 --
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 2.0397 2.0906 -- 109 1281 0.2679 0.3396 0.0 75.0
X Ray Diffraction 2.0906 2.1471 -- 133 1576 0.232 0.2934 0.0 91.0
X Ray Diffraction 2.1471 2.2102 -- 145 1708 0.2259 0.2894 0.0 99.0
X Ray Diffraction 2.2102 2.2814 -- 145 1721 0.2126 0.3046 0.0 99.0
X Ray Diffraction 2.2814 2.3628 -- 143 1708 0.2191 0.3004 0.0 99.0
X Ray Diffraction 2.3628 2.4572 -- 146 1731 0.2223 0.2959 0.0 99.0
X Ray Diffraction 2.4572 2.5688 -- 146 1720 0.2287 0.3274 0.0 99.0
X Ray Diffraction 2.5688 2.7039 -- 145 1717 0.236 0.2952 0.0 99.0
X Ray Diffraction 2.7039 2.8728 -- 143 1706 0.2567 0.3521 0.0 98.0
X Ray Diffraction 2.8728 3.0938 -- 144 1696 0.2454 0.3289 0.0 97.0
X Ray Diffraction 3.0938 3.4036 -- 147 1740 0.1836 0.2311 0.0 100.0
X Ray Diffraction 3.4036 3.8925 -- 150 1767 0.1533 0.1895 0.0 100.0
X Ray Diffraction 3.8925 4.8909 -- 146 1717 0.1468 0.191 0.0 98.0
X Ray Diffraction 4.8909 19.2833 -- 149 1772 0.1602 0.2044 0.0 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.3015
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.049
f_dihedral_angle_d 18.489
f_bond_d 0.008
f_plane_restr 0.005
f_angle_d 0.913
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2614
Nucleic Acid Atoms 629
Heterogen Atoms 37
Solvent Atoms 311

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