4DU3

RB69 DNA Polymerase Ternary Complex with dDTP Opposite dT with 3-Deaza-adenine at the N-1 Position of Template Strand


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.5298100 mM CaCl2, 15% (w/v) PEG 350 monomethyl ether (MME), 100 mM Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5551.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.641α = 90
b = 120.176β = 90
c = 130.067γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDAPEX II CCD2011-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.97918APS24-ID-E

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
12.025094.676820726942.21.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.022.0999.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.0249.0372694384799.060.192590.190780.22656RANDOM38.407
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]
-1.130.910.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.586
r_dihedral_angle_3_deg14.219
r_dihedral_angle_4_deg11.859
r_dihedral_angle_1_deg5.187
r_scangle_it4.103
r_scbond_it2.762
r_mcangle_it2.398
r_mcbond_it1.44
r_angle_refined_deg1.165
r_chiral_restr0.085
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.586
r_dihedral_angle_3_deg14.219
r_dihedral_angle_4_deg11.859
r_dihedral_angle_1_deg5.187
r_scangle_it4.103
r_scbond_it2.762
r_mcangle_it2.398
r_mcbond_it1.44
r_angle_refined_deg1.165
r_chiral_restr0.085
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7355
Nucleic Acid Atoms628
Solvent Atoms537
Heterogen Atoms37

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling