5L1I

Crystal Structure of Human DNA Polymerase Eta Inserting dCTP 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 Calcium chloride, 15% PEG 2000 MME
Crystal Properties
Matthews coefficientSolvent content
2.1141.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.095α = 90
b = 99.095β = 90
c = 81.869γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2014-06-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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
12.785099.90.1690.16910.6475.511577-3
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)
12.782.8499.80.9661.5795.2

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 REPLACEMENTTHROUGHOUT4O3N2.78501096259499.910.163530.159940.22835RANDOM49.131
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]
-0.12-0.06-0.120.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.649
r_dihedral_angle_4_deg19.129
r_dihedral_angle_3_deg16.267
r_long_range_B_refined8.01
r_long_range_B_other7.994
r_dihedral_angle_1_deg6.775
r_scangle_other5
r_mcangle_it4.847
r_mcangle_other4.846
r_scbond_it3.096
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.649
r_dihedral_angle_4_deg19.129
r_dihedral_angle_3_deg16.267
r_long_range_B_refined8.01
r_long_range_B_other7.994
r_dihedral_angle_1_deg6.775
r_scangle_other5
r_mcangle_it4.847
r_mcangle_other4.846
r_scbond_it3.096
r_scbond_other3.093
r_mcbond_it2.948
r_mcbond_other2.948
r_angle_refined_deg1.523
r_angle_other_deg1.038
r_chiral_restr0.08
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms409
Solvent Atoms138
Heterogen Atoms42

Software

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