6CTK

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHF-R/S isomers, 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 = 50.64 α = 90
b = 79.24 β = 107.08
c = 55.38 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 -- 2014-05-12
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
2.1 50 98.7 0.069 -- -- 3.4 -- 22680 -- -- 34.94
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)
2.1 2.18 89.2 0.487 -- -- 2.7 --

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 2.153 21.237 -- 1.33 -- 22519 1987 99.12 -- 0.1846 0.1787 0.244 --
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 2.153 2.2067 -- 140 1450 0.2574 0.321 0.0 99.0
X Ray Diffraction 2.2067 2.2663 -- 142 1464 0.239 0.3244 0.0 100.0
X Ray Diffraction 2.2663 2.3329 -- 144 1483 0.2481 0.3338 0.0 100.0
X Ray Diffraction 2.3329 2.4081 -- 144 1488 0.2379 0.3251 0.0 100.0
X Ray Diffraction 2.4081 2.4941 -- 138 1435 0.2434 0.3263 0.0 100.0
X Ray Diffraction 2.4941 2.5938 -- 141 1462 0.2531 0.3352 0.0 99.0
X Ray Diffraction 2.5938 2.7116 -- 140 1463 0.251 0.312 0.0 99.0
X Ray Diffraction 2.7116 2.8543 -- 142 1464 0.2693 0.4043 0.0 98.0
X Ray Diffraction 2.8543 3.0326 -- 138 1431 0.2553 0.3773 0.0 97.0
X Ray Diffraction 3.0326 3.266 -- 142 1456 0.1949 0.258 0.0 100.0
X Ray Diffraction 3.266 3.5932 -- 144 1487 0.1439 0.2245 0.0 100.0
X Ray Diffraction 3.5932 4.1099 -- 142 1458 0.1425 0.1964 0.0 99.0
X Ray Diffraction 4.1099 5.1657 -- 142 1471 0.1306 0.171 0.0 98.0
X Ray Diffraction 5.1657 21.2377 -- 148 1520 0.1228 0.1666 0.0 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.6754
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.059
f_plane_restr 0.005
f_chiral_restr 0.042
f_dihedral_angle_d 21.077
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2608
Nucleic Acid Atoms 630
Heterogen Atoms 34
Solvent Atoms 228

Software

Software
Software Name Purpose
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX refinement version: 1.9_1692
PDB_EXTRACT data extraction version: 3.24
PHENIX phasing