2FLL

Ternary complex of human DNA polymerase iota with DNA and dTTP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AZLPDB code 2AZL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5pH 6.5, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.6854.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.329α = 90
b = 98.329β = 90
c = 202.186γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-IDAPS17-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
12.65099.70.05934.571851718496

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB code 2AZL2.6501851716057137694.190.227650.223290.27747RANDOM42.281
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]
0.630.310.63-0.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.705
r_scangle_it5.62
r_scbond_it3.822
r_mcangle_it3.288
r_angle_refined_deg2.929
r_mcbond_it1.951
r_angle_other_deg1.522
r_symmetry_vdw_refined0.616
r_symmetry_vdw_other0.44
r_symmetry_hbond_refined0.436
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.705
r_scangle_it5.62
r_scbond_it3.822
r_mcangle_it3.288
r_angle_refined_deg2.929
r_mcbond_it1.951
r_angle_other_deg1.522
r_symmetry_vdw_refined0.616
r_symmetry_vdw_other0.44
r_symmetry_hbond_refined0.436
r_nbd_other0.277
r_nbd_refined0.264
r_xyhbond_nbd_refined0.196
r_chiral_restr0.177
r_nbtor_other0.105
r_bond_refined_d0.043
r_gen_planes_refined0.016
r_gen_planes_other0.014
r_bond_other_d0.003
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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 Atoms2866
Nucleic Acid Atoms321
Solvent Atoms91
Heterogen Atoms31

Software

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