5L1K

PostInsertion complex of Human DNA Polymerase Eta bypassing an O6-Methyl-2'-deoxyguanosine : dC 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
2.141.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.459α = 90
b = 98.459β = 90
c = 82.112γ = 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
11.82501000.1180.11814.5535.740671-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.821.851000.8090.8091.8465.6

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 REPLACEMENTTHROUGHOUT4O3N1.825038540209599.950.154430.152520.18756RANDOM23.887
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]
0.060.030.06-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.301
r_dihedral_angle_4_deg17.337
r_dihedral_angle_3_deg14.18
r_long_range_B_refined8.028
r_long_range_B_other7.899
r_dihedral_angle_1_deg5.971
r_scangle_other4.992
r_mcangle_other3.527
r_mcangle_it3.525
r_scbond_it3.239
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.301
r_dihedral_angle_4_deg17.337
r_dihedral_angle_3_deg14.18
r_long_range_B_refined8.028
r_long_range_B_other7.899
r_dihedral_angle_1_deg5.971
r_scangle_other4.992
r_mcangle_other3.527
r_mcangle_it3.525
r_scbond_it3.239
r_scbond_other3.239
r_mcbond_it2.288
r_mcbond_other2.282
r_angle_refined_deg1.893
r_angle_other_deg1.584
r_chiral_restr0.118
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 Atoms390
Solvent Atoms491
Heterogen Atoms36

Software

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