5TBC

PRECATALYTIC TERNARY COMPLEX OF HUMAN DNA POLYMERASE BETA WITH GAPPED DNA SUBSTRATE, INCORPORATED (-)3TC-MP AND AN ANOTHER INCOMING (-)3TC-TP NUCLEOTIDE.


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
2.3848.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.33α = 90
b = 79.53β = 107.39
c = 55.33γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray193CCDRAYONIX MX225HE2014-04-05MSINGLE 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
11.8532.7698.90.0888.43.838657
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)
11.851.8998.70.68623.8

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 REPLACEMENTTHROUGHOUT4RQ71.8532.7636763188398.80.2310.2280.279RANDOM32.22
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]
0.360.210.08-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.87
r_dihedral_angle_3_deg14.665
r_dihedral_angle_4_deg12.188
r_dihedral_angle_1_deg5.035
r_long_range_B_refined4.973
r_long_range_B_other4.829
r_scangle_other2.833
r_mcangle_it2.7
r_mcangle_other2.699
r_scbond_it1.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.87
r_dihedral_angle_3_deg14.665
r_dihedral_angle_4_deg12.188
r_dihedral_angle_1_deg5.035
r_long_range_B_refined4.973
r_long_range_B_other4.829
r_scangle_other2.833
r_mcangle_it2.7
r_mcangle_other2.699
r_scbond_it1.73
r_scbond_other1.73
r_mcbond_other1.576
r_mcbond_it1.575
r_angle_refined_deg1.162
r_chiral_restr0.07
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_gen_planes_other0.001
r_bond_other_d
r_angle_other_deg
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 Atoms2354
Nucleic Acid Atoms632
Solvent Atoms252
Heterogen Atoms52

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement