6CR7

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHF, 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 = 50.17 α = 90
b = 79.06 β = 107.05
c = 55.61 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 MARMOSAIC 225 mm CCD -- 2015-04-10
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 0.9999 APS 22-BM

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
2.29 20 84.8 -- -- -- 3.3 -- 15814 -- -- --
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)
2.3 2.34 34.8 -- -- -- 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 2.29 19.795 -- 1.36 -- 15802 1580 84.24 -- 0.1803 0.1738 0.2403 --
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 2.2902 2.364 -- 55 501 0.2625 0.3454 0.0 32.0
X Ray Diffraction 2.364 2.4484 -- 82 731 0.2364 0.3331 0.0 49.0
X Ray Diffraction 2.4484 2.5462 -- 114 1028 0.2383 0.3159 0.0 67.0
X Ray Diffraction 2.5462 2.6618 -- 142 1279 0.2388 0.2902 0.0 84.0
X Ray Diffraction 2.6618 2.8018 -- 161 1448 0.2282 0.3191 0.0 95.0
X Ray Diffraction 2.8018 2.9768 -- 170 1523 0.2149 0.2868 0.0 100.0
X Ray Diffraction 2.9768 3.2058 -- 169 1525 0.2117 0.2738 0.0 100.0
X Ray Diffraction 3.2058 3.5267 -- 171 1543 0.1769 0.263 0.0 100.0
X Ray Diffraction 3.5267 4.0333 -- 170 1530 0.1503 0.2206 0.0 100.0
X Ray Diffraction 4.0333 5.0674 -- 173 1549 0.1356 0.1813 0.0 100.0
X Ray Diffraction 5.0674 19.7961 -- 173 1565 0.1404 0.204 0.0 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 40.8207
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 19.172
f_bond_d 0.008
f_plane_restr 0.005
f_angle_d 1.162
f_chiral_restr 0.086
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2614
Nucleic Acid Atoms 629
Heterogen Atoms 38
Solvent Atoms 137

Software

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