4DTX

RB69 DNA Polymerase Ternary Complex with dTTP Opposite an Abasic Site and ddC/dG as the Penultimate Base-pair


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
2.6253.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.414α = 90
b = 120.208β = 90
c = 131.619γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDAPEX II CCD2010-09-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.98918APS24-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
11.845094.79492131.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.841.8780.2

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 REPLACEMENTTHROUGHOUT1.8435.3894920499395.960.171730.169910.20589RANDOM32.579
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]
-0.140.64-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.038
r_dihedral_angle_4_deg14.968
r_dihedral_angle_3_deg13.816
r_dihedral_angle_1_deg5.161
r_scangle_it4.148
r_scbond_it2.714
r_mcangle_it2.303
r_mcbond_it1.323
r_angle_refined_deg1.169
r_chiral_restr0.085
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.038
r_dihedral_angle_4_deg14.968
r_dihedral_angle_3_deg13.816
r_dihedral_angle_1_deg5.161
r_scangle_it4.148
r_scbond_it2.714
r_mcangle_it2.303
r_mcbond_it1.323
r_angle_refined_deg1.169
r_chiral_restr0.085
r_bond_refined_d0.007
r_gen_planes_refined0.005
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 Atoms7343
Nucleic Acid Atoms620
Solvent Atoms795
Heterogen Atoms33

Software

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