X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 291.0
Details 200 microM Dpo4, 240 microM primer-template DNA complex, 5 mM MgCl2, 1 mM dTTP, 20 mM Tris-HCl (pH 7.4), 60 mM NaCl, 2% glycerol (v/v), and 5 mM 2-mercaptoethanol were incubated at 37 C for 5 min. Droplets (a 1:1 mixture of Dpo4-DNA complex mixture and the reservoir solution, v/v) were equilibrated against a reservoir solution containing 0.1M Tris-HCl (pH 7.4), 13% polyethylene glycol 3350 (w/v), 0.1 M Ca(CH3COO)2, and 2% glycerol (v/v).

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 58.54 α = 90
b = 89.41 β = 90
c = 112.39 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2014-03-28
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 1.0 APS 21-ID-F

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
1.58 28.32 99.7 -- -- -- 5.5 -- 81191 -- -- --
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)
1.58 1.6 99.9 -- -- 2.9 5.0 --

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
-- 1.58 28.32 -- 1.34 -- 81191 4024 99.68 -- 0.183 0.182 0.2022 --
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 1.58 1.5986 -- 119 2649 0.239 0.2406 -- 100.0
X Ray Diffraction 1.5986 1.6181 -- 144 2623 0.2278 0.2404 -- 100.0
X Ray Diffraction 1.6181 1.6386 -- 135 2627 0.2214 0.2687 -- 100.0
X Ray Diffraction 1.6386 1.6601 -- 134 2627 0.2122 0.215 -- 100.0
X Ray Diffraction 1.6601 1.6829 -- 142 2644 0.2054 0.2482 -- 100.0
X Ray Diffraction 1.6829 1.7069 -- 154 2632 0.1948 0.2285 -- 100.0
X Ray Diffraction 1.7069 1.7324 -- 139 2649 0.1999 0.2199 -- 100.0
X Ray Diffraction 1.7324 1.7594 -- 158 2614 0.201 0.228 -- 100.0
X Ray Diffraction 1.7594 1.7883 -- 135 2650 0.195 0.2319 -- 100.0
X Ray Diffraction 1.7883 1.8191 -- 137 2639 0.1943 0.2255 -- 100.0
X Ray Diffraction 1.8191 1.8522 -- 150 2605 0.19 0.19 -- 100.0
X Ray Diffraction 1.8522 1.8878 -- 136 2702 0.199 0.2267 -- 100.0
X Ray Diffraction 1.8878 1.9263 -- 127 2600 0.1896 0.2219 -- 100.0
X Ray Diffraction 1.9263 1.9682 -- 112 2691 0.1917 0.2254 -- 100.0
X Ray Diffraction 1.9682 2.014 -- 161 2659 0.1871 0.1947 -- 100.0
X Ray Diffraction 2.014 2.0643 -- 139 2643 0.1891 0.2241 -- 100.0
X Ray Diffraction 2.0643 2.1201 -- 126 2664 0.1884 0.1938 -- 100.0
X Ray Diffraction 2.1201 2.1825 -- 137 2687 0.1747 0.177 -- 100.0
X Ray Diffraction 2.1825 2.2529 -- 124 2658 0.1807 0.1801 -- 100.0
X Ray Diffraction 2.2529 2.3334 -- 132 2662 0.1817 0.1787 -- 100.0
X Ray Diffraction 2.3334 2.4268 -- 141 2694 0.1868 0.2174 -- 100.0
X Ray Diffraction 2.4268 2.5372 -- 145 2664 0.1904 0.219 -- 100.0
X Ray Diffraction 2.5372 2.6708 -- 147 2684 0.1953 0.2131 -- 100.0
X Ray Diffraction 2.6708 2.838 -- 146 2646 0.1923 0.2348 -- 100.0
X Ray Diffraction 2.838 3.0569 -- 155 2715 0.2004 0.197 -- 100.0
X Ray Diffraction 3.0569 3.3641 -- 135 2699 0.1767 0.1852 -- 100.0
X Ray Diffraction 3.3641 3.8498 -- 137 2727 0.1647 0.1834 -- 100.0
X Ray Diffraction 3.8498 4.8464 -- 153 2735 0.1504 0.1945 -- 99.0
X Ray Diffraction 4.8464 28.3284 -- 124 2678 0.1809 0.1904 -- 92.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.1726
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.007
f_plane_restr 0.005
f_chiral_restr 0.045
f_angle_d 1.158
f_dihedral_angle_d 18.755
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2658
Nucleic Acid Atoms 609
Heterogen Atoms 52
Solvent Atoms 561

Software

Software
Software Name Purpose
PDB_EXTRACT data extraction version: 3.14
PHENIX refinement version: (phenix.refine: 1.9_1690)