5TB8

Precatalytic ternary complex of Human DNA Polymerase Beta in closed conformation With Gapped DNA substrate incoming (-)3TC-TP and Mn2+.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829550 MM IMIDAZOLE, 350 MM SODIUM ACETATE, 17% PEG3350, PH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.0840.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.48α = 90
b = 81.4β = 110.28
c = 53.57γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray193CCDRAYONIX MX225HE2014-12-03MSINGLE 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
1246.4198.20.1096.43.326398
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)
122.0597.60.43323

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 REPLACEMENTTHROUGHOUT4RPX246.4125091128797.70.1840.1820.23RANDOM22.35
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]
0.05-0.05-0.040.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.394
r_dihedral_angle_4_deg15.121
r_dihedral_angle_3_deg14.664
r_dihedral_angle_1_deg6.392
r_long_range_B_refined5.385
r_long_range_B_other5.348
r_scangle_other3.733
r_mcangle_it2.602
r_mcangle_other2.601
r_scbond_it2.452
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.394
r_dihedral_angle_4_deg15.121
r_dihedral_angle_3_deg14.664
r_dihedral_angle_1_deg6.392
r_long_range_B_refined5.385
r_long_range_B_other5.348
r_scangle_other3.733
r_mcangle_it2.602
r_mcangle_other2.601
r_scbond_it2.452
r_scbond_other2.452
r_angle_refined_deg1.696
r_mcbond_it1.646
r_mcbond_other1.63
r_angle_other_deg1.137
r_chiral_restr0.099
r_bond_refined_d0.014
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 Atoms2639
Nucleic Acid Atoms632
Solvent Atoms201
Heterogen Atoms64

Software

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