X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP291220 microM Dpo4, 264 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), 15% polyethylene glycol 3350 (w/v), 0.1 M Ca(CH3COO)2, and 2% glycerol (v/v).
Crystal Properties
Matthews coefficientSolvent content
2.550.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.12α = 90
b = 184.242β = 110.09
c = 52.124γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARMOSAIC 225 mm CCD2014-03-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F1.0APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.0628.40798.525886020.37
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.062.198.533.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONFREE R-VALUE2.0628.4071.3955908271798.520.23120.22820.289926.3748
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d19.73
f_angle_d1.147
f_chiral_restr0.044
f_bond_d0.009
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5221
Nucleic Acid Atoms1044
Solvent Atoms488
Heterogen Atoms96

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
Cootmodel building
MOLREPphasing
PDB_EXTRACTdata extraction