5U2T

Pre-catalytic ternary complex of Human DNA Polymerase Beta With Gapped DNA substrate incoming (-)FTC-TP and Ca2+.


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
Crystal Properties
Matthews coefficientSolvent content
2.3247.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.615α = 90
b = 79.395β = 107.6
c = 54.795γ = 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
11.7915.7899.30.06919.755.641380
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)
11.81.861000.7782.465.6

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 REPLACEMENTTHROUGHOUT4RQ71.7915.78392172076990.2020.20.247RANDOM44.31
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]
-0.440.34-0.460.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.13
r_dihedral_angle_4_deg14.289
r_dihedral_angle_3_deg13.716
r_long_range_B_refined6.621
r_long_range_B_other6.549
r_dihedral_angle_1_deg5.85
r_scangle_other4.564
r_mcangle_it3.972
r_mcangle_other3.972
r_scbond_it3.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.13
r_dihedral_angle_4_deg14.289
r_dihedral_angle_3_deg13.716
r_long_range_B_refined6.621
r_long_range_B_other6.549
r_dihedral_angle_1_deg5.85
r_scangle_other4.564
r_mcangle_it3.972
r_mcangle_other3.972
r_scbond_it3.001
r_scbond_other3.001
r_mcbond_it2.747
r_mcbond_other2.741
r_angle_refined_deg1.458
r_angle_other_deg1.105
r_chiral_restr0.092
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 Atoms2592
Nucleic Acid Atoms632
Solvent Atoms242
Heterogen Atoms46

Software

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