2FLP

Binary complex of the catalytic core of human DNA polymerase iota with DNA (template G)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ALZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5pH 6.5, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.6854.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.367α = 90
b = 98.367β = 90
c = 202.497γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-IDAPS19-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
12.45098.30.05516.510.32310722540

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 ALZ2.436.512310720314222496.220.23280.228030.27616RANDOM45.563
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]
0.30.150.3-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.312
r_scangle_it5.852
r_scbond_it4.239
r_mcangle_it3.37
r_angle_refined_deg3.182
r_mcbond_it2.018
r_symmetry_hbond_refined0.516
r_symmetry_vdw_refined0.407
r_nbd_refined0.301
r_xyhbond_nbd_refined0.228
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.312
r_scangle_it5.852
r_scbond_it4.239
r_mcangle_it3.37
r_angle_refined_deg3.182
r_mcbond_it2.018
r_symmetry_hbond_refined0.516
r_symmetry_vdw_refined0.407
r_nbd_refined0.301
r_xyhbond_nbd_refined0.228
r_chiral_restr0.213
r_bond_refined_d0.06
r_gen_planes_refined0.014
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_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 Atoms2813
Nucleic Acid Atoms322
Solvent Atoms115
Heterogen Atoms

Software

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