4M8O

TERNARY COMPLEX OF DNA POLYMERASE EPSILON WITH AN INCOMING dATP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IAYPDB ENTRY 3IAY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729120% PEG-3350, 50 mM Hepes-NaOH pH 7.0, 10 mM MgCl2, 400 mM LiAc, and 10 mM 2-aminoethanesulfonic acid (taurine) , VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.3948.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 148.495α = 90
b = 68.919β = 109.5
c = 149.852γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2012-10-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.873ESRFID23-2

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
12.247.0599.969054
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)
12.22.3299.80.5482.53.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3IAY2.247.056905469054366799.90.1830.180.237RANDOM38.06
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]
-0.02-0.241.03-0.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.084
r_dihedral_angle_3_deg17.558
r_dihedral_angle_4_deg16.981
r_long_range_B_refined8.581
r_long_range_B_other8.58
r_dihedral_angle_1_deg6.904
r_scangle_other6.071
r_mcangle_it5.009
r_mcangle_other5.009
r_scbond_it3.908
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.084
r_dihedral_angle_3_deg17.558
r_dihedral_angle_4_deg16.981
r_long_range_B_refined8.581
r_long_range_B_other8.58
r_dihedral_angle_1_deg6.904
r_scangle_other6.071
r_mcangle_it5.009
r_mcangle_other5.009
r_scbond_it3.908
r_scbond_other3.908
r_mcbond_it3.282
r_mcbond_other3.28
r_angle_refined_deg1.866
r_angle_other_deg0.912
r_chiral_restr0.105
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9173
Nucleic Acid Atoms535
Solvent Atoms459
Heterogen Atoms48

Software

Software
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling