X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IHMhPol Mu Loop2 truncation variant in ternary complex with single-nucleotide gapped DNA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5277Crystals were grown by mixing 1uL of the protein/DNA complex with 1uL of mother liquor (85mM MES pH 6.5, 85mMCaCl2, 42.5mM NaCl, 8.5% PEG3350, 11% glycerol), using the sitting drop vapor diffusion technique. Crystals were transferred to a cryoprotectant solution containing 0.1M MES pH 6.5, 0.1M CaCl2, 50mM NaCl, 10mM MgCl2, 20% PEG3350, 15% glycerol in three steps. , VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.5150.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.003α = 90
b = 68.514β = 90
c = 110.307γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDMARMOSAIC 300 mm CCD2012-10-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (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
11.5995098.60.06213.86.26003360033-317.45
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.5991.6383.10.2722.42520

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUThPol Mu Loop2 truncation variant in ternary complex with single-nucleotide gapped DNA1.59934.9321.346003359953299198.510.180.1750.17420.2046random14.6934
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_d13.129
f_angle_d1.448
f_chiral_restr0.095
f_bond_d0.011
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2551
Nucleic Acid Atoms344
Solvent Atoms513
Heterogen Atoms10

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
HKL-2000data reduction