5L1J

Crystal Structure of Human DNA Polymerase Eta Inserting dTMPNPP Opposite O6-Methyl-2'-deoxyguanosine


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 Magnesium chloride, 16% PEG 2000 MME
Crystal Properties
Matthews coefficientSolvent content
2.1141.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.004α = 90
b = 99.004β = 90
c = 81.704γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2013-08-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.07810APS21-ID-D

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
11.94501000.0910.09127.3757.633771-3
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)
11.941.971000.8192.5487.5

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 REPLACEMENTTHROUGHOUT4O3N1.945032023171599.980.16080.158570.20166RANDOM33.677
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]
-0.16-0.08-0.160.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.435
r_dihedral_angle_4_deg15.404
r_dihedral_angle_3_deg14.963
r_long_range_B_refined8.152
r_long_range_B_other8.017
r_dihedral_angle_1_deg6.275
r_scangle_other5.541
r_mcangle_it4.228
r_mcangle_other4.227
r_scbond_it3.769
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.435
r_dihedral_angle_4_deg15.404
r_dihedral_angle_3_deg14.963
r_long_range_B_refined8.152
r_long_range_B_other8.017
r_dihedral_angle_1_deg6.275
r_scangle_other5.541
r_mcangle_it4.228
r_mcangle_other4.227
r_scbond_it3.769
r_scbond_other3.768
r_mcbond_other3.013
r_mcbond_it3.012
r_angle_refined_deg1.886
r_angle_other_deg1.132
r_chiral_restr0.115
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms410
Heterogen Atoms37

Software

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