3EPG

Structure of Human DNA Polymerase Iota complexed with N2-ethylguanine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ALZ2ALZ minus DNA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5277.1512-15% PEG MME 5000, 0.2-0.4M Ammonium Sulfate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Crystal Properties
Matthews coefficientSolvent content
2.4449.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.535α = 90
b = 98.535β = 90
c = 202.354γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVConfocal2006-11-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

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
12.21598.90.1221317.773015019625
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)
12.22.2890.60.45.111.73

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 REPLACEMENTTHROUGHOUT2ALZ minus DNA2.51519625104699.070.236710.234350.28284RANDOM34.125
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]
0.480.240.48-0.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.711
r_dihedral_angle_4_deg20.628
r_dihedral_angle_3_deg19.237
r_dihedral_angle_1_deg6.83
r_scangle_it2.519
r_angle_refined_deg1.806
r_scbond_it1.574
r_mcangle_it0.968
r_mcbond_it0.516
r_symmetry_vdw_refined0.431
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.711
r_dihedral_angle_4_deg20.628
r_dihedral_angle_3_deg19.237
r_dihedral_angle_1_deg6.83
r_scangle_it2.519
r_angle_refined_deg1.806
r_scbond_it1.574
r_mcangle_it0.968
r_mcbond_it0.516
r_symmetry_vdw_refined0.431
r_nbtor_refined0.306
r_symmetry_hbond_refined0.301
r_nbd_refined0.247
r_xyhbond_nbd_refined0.203
r_chiral_restr0.138
r_bond_refined_d0.015
r_gen_planes_refined0.005
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 Atoms2896
Nucleic Acid Atoms310
Solvent Atoms69
Heterogen Atoms32

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling