3G6X

Ternary complex of DNA Polymerase iota:DNA:dGTP with an abasic site at the templating position


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293Crystals grew in 24 hours, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6954.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.114α = 90
b = 98.114β = 90
c = 202.823γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210Si(111) double-crystal monochromator2005-07-18MSINGLE 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
12.0850940.04932.69.93503033090
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)
12.082.151000.2449.910.5

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 REPLACEMENTTHROUGHOUT2FLL2.08203503031309276096.140.225390.221970.2647RANDOM28.368
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]
0.560.280.56-0.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.996
r_dihedral_angle_4_deg24.665
r_dihedral_angle_3_deg19.444
r_dihedral_angle_1_deg6.658
r_scangle_it4.53
r_scbond_it3.048
r_angle_refined_deg2.22
r_mcangle_it1.918
r_mcbond_it1.079
r_symmetry_vdw_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.996
r_dihedral_angle_4_deg24.665
r_dihedral_angle_3_deg19.444
r_dihedral_angle_1_deg6.658
r_scangle_it4.53
r_scbond_it3.048
r_angle_refined_deg2.22
r_mcangle_it1.918
r_mcbond_it1.079
r_symmetry_vdw_refined0.315
r_nbtor_refined0.297
r_symmetry_hbond_refined0.238
r_nbd_refined0.236
r_xyhbond_nbd_refined0.22
r_chiral_restr0.187
r_bond_refined_d0.023
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
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 Atoms2876
Nucleic Acid Atoms294
Solvent Atoms219
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
AMoREphasing
CNSrefinement
JDirectordata collection
HKL-2000data reduction
HKL-2000data scaling