5TBA

Postcatalytic ternary complex of Human DNA Polymerase Beta with Gapped DNA substrate, incorporated (-)3TC and PPi.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4RQ7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829550 MM IMIDAZOLE, 350 MM SODIUM ACETATE, 17% PEG3350 , PH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.3447.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.697α = 90
b = 79.325β = 107.03
c = 54.947γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray193CCDRAYONIX MX225HE2013-10-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.97931APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.4925.1899.60.16811.95.615629
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)
12.52.591000.7085.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT4RQ72.4925.181483178199.10.2080.2050.273RANDOM41.5
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]
-0.14-0.120.060.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.345
r_dihedral_angle_4_deg19.166
r_dihedral_angle_3_deg16.114
r_long_range_B_other6.752
r_long_range_B_refined6.75
r_dihedral_angle_1_deg6.516
r_mcangle_it4.632
r_mcangle_other4.631
r_scangle_other4.247
r_mcbond_other2.782
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.345
r_dihedral_angle_4_deg19.166
r_dihedral_angle_3_deg16.114
r_long_range_B_other6.752
r_long_range_B_refined6.75
r_dihedral_angle_1_deg6.516
r_mcangle_it4.632
r_mcangle_other4.631
r_scangle_other4.247
r_mcbond_other2.782
r_mcbond_it2.781
r_scbond_it2.735
r_scbond_other2.735
r_angle_refined_deg1.464
r_angle_other_deg0.897
r_chiral_restr0.074
r_bond_refined_d0.01
r_gen_planes_refined0.007
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 Atoms2537
Nucleic Acid Atoms632
Solvent Atoms59
Heterogen Atoms32

Software

Software
Software NamePurpose
HKL-2000data reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement