6CRB

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CF2, 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 = 54.76 α = 90
b = 78.77 β = 108.78
c = 54.47 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 944 -- 2015-04-10
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
2.15 20 95.0 0.074 -- -- 3.6 -- 22684 -- -- --
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)
2.15 2.19 72.3 0.457 -- -- 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 2.151 19.973 -- 1.33 -- 22653 2004 94.93 -- 0.2227 0.2175 0.2748 --
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 2.1512 2.205 -- 111 1139 0.2773 0.3474 0.0 73.0
X Ray Diffraction 2.205 2.2645 -- 124 1267 0.2585 0.321 0.0 82.0
X Ray Diffraction 2.2645 2.3311 -- 126 1342 0.2657 0.3234 0.0 87.0
X Ray Diffraction 2.3311 2.4062 -- 140 1444 0.263 0.3285 0.0 93.0
X Ray Diffraction 2.4062 2.492 -- 148 1507 0.2794 0.3816 0.0 97.0
X Ray Diffraction 2.492 2.5916 -- 147 1543 0.266 0.3269 0.0 99.0
X Ray Diffraction 2.5916 2.7093 -- 143 1520 0.2757 0.3414 0.0 99.0
X Ray Diffraction 2.7093 2.8517 -- 154 1533 0.2804 0.3423 0.0 99.0
X Ray Diffraction 2.8517 3.0298 -- 149 1567 0.2786 0.3991 0.0 100.0
X Ray Diffraction 3.0298 3.2628 -- 148 1536 0.2417 0.2854 0.0 100.0
X Ray Diffraction 3.2628 3.5895 -- 150 1549 0.1955 0.2659 0.0 100.0
X Ray Diffraction 3.5895 4.105 -- 154 1549 0.1877 0.2622 0.0 99.0
X Ray Diffraction 4.105 5.157 -- 153 1561 0.1814 0.2173 0.0 100.0
X Ray Diffraction 5.157 19.9739 -- 157 1592 0.1701 0.1945 0.0 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 44.3399
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.269
f_bond_d 0.009
f_plane_restr 0.006
f_chiral_restr 0.062
f_dihedral_angle_d 20.941
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2602
Nucleic Acid Atoms 628
Heterogen Atoms 36
Solvent Atoms 175

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