6CTP

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CH2, 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 = 50.28 α = 90
b = 78.92 β = 106.98
c = 55.35 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 -- 2015-04-29
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
2.2 20 99.3 0.12 -- -- 3.3 -- 21114 -- -- --
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)
2.2 2.28 99.9 0.73 -- -- 3.3 --

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 2.2 19.819 -- 1.33 -- 20680 1956 96.8 -- 0.2309 0.2247 0.2901 --
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 2.1886 2.2432 -- 131 1250 0.3594 0.4248 0.0 92.0
X Ray Diffraction 2.2432 2.3038 -- 144 1367 0.3197 0.3808 0.0 99.0
X Ray Diffraction 2.3038 2.3715 -- 141 1346 0.2967 0.3675 0.0 100.0
X Ray Diffraction 2.3715 2.4479 -- 142 1351 0.2947 0.3589 0.0 98.0
X Ray Diffraction 2.4479 2.5352 -- 145 1362 0.3018 0.382 0.0 98.0
X Ray Diffraction 2.5352 2.6365 -- 139 1356 0.3166 0.474 0.0 97.0
X Ray Diffraction 2.6365 2.7562 -- 134 1278 0.3396 0.2974 0.0 94.0
X Ray Diffraction 2.7562 2.9011 -- 127 1236 0.3416 0.4346 0.0 90.0
X Ray Diffraction 2.9011 3.0822 -- 132 1266 0.3218 0.3989 0.0 92.0
X Ray Diffraction 3.0822 3.3192 -- 145 1389 0.2396 0.309 0.0 100.0
X Ray Diffraction 3.3192 3.6513 -- 144 1375 0.1858 0.2572 0.0 100.0
X Ray Diffraction 3.6513 4.1754 -- 142 1371 0.1835 0.2528 0.0 98.0
X Ray Diffraction 4.1754 5.2444 -- 141 1357 0.1825 0.2253 0.0 98.0
X Ray Diffraction 5.2444 19.8203 -- 149 1420 0.157 0.221 0.0 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 46.017
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.053
f_bond_d 0.009
f_plane_restr 0.006
f_angle_d 1.031
f_dihedral_angle_d 20.865
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2608
Nucleic Acid Atoms 630
Heterogen Atoms 36
Solvent Atoms 107

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