5L1L

PostInsertion complex of Human DNA Polymerase Eta bypassing an O6-Methyl-2'-deoxyguanosine : dT site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4O3N 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52910.1 M MES pH 5.5, 5mM Calcium chloride, 18% PEG 2000 MME
Crystal Properties
Matthews coefficientSolvent content
2.0941.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.355α = 90
b = 98.355β = 90
c = 82.034γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2013-07-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.62501000.0980.09823.1767.657284-3
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)
11.621.651000.8692.0367.2

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 REPLACEMENTTHROUGHOUT4O3N1.625054491275899.980.158550.156790.19348RANDOM24.47
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]
0.020.010.02-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.416
r_dihedral_angle_4_deg18.45
r_dihedral_angle_3_deg13.824
r_long_range_B_refined7.863
r_long_range_B_other7.863
r_dihedral_angle_1_deg5.778
r_scangle_other4.889
r_scbond_it3.2
r_scbond_other3.2
r_mcangle_other3.087
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.416
r_dihedral_angle_4_deg18.45
r_dihedral_angle_3_deg13.824
r_long_range_B_refined7.863
r_long_range_B_other7.863
r_dihedral_angle_1_deg5.778
r_scangle_other4.889
r_scbond_it3.2
r_scbond_other3.2
r_mcangle_other3.087
r_mcangle_it3.086
r_mcbond_it2.079
r_mcbond_other2.078
r_angle_refined_deg1.881
r_angle_other_deg1.631
r_chiral_restr0.125
r_bond_refined_d0.018
r_gen_planes_refined0.011
r_gen_planes_other0.003
r_bond_other_d0.002
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 Atoms3366
Nucleic Acid Atoms391
Solvent Atoms526
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing