8UJV

Crystal structure of human polymerase eta with incoming dCMPnPP nucleotide opposite urea lesion


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5F9NCRYSTAL STRUCTURE OF HUMAN DNA POLYMERASE ETA INSERTING dCMPNPP ACROSS A DNA TEMPLATE CONTAINING 1,N2-ETHENODEOXYGUANOSINE LESION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52910.1 M MES pH 5.5, 5mM magnesium chloride, 18% PEG 2000 MME
Crystal Properties
Matthews coefficientSolvent content
2.141.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.951α = 90
b = 98.951β = 90
c = 81.498γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002022-10-13MSINGLE 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)Rpim I (All)CC (Half)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
12.23501000.070.070.040.99423.64.122232
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.232.271000.40.40.20.813.244

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.2349.481.3522187105499.880.16850.16580.2224
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d19.683
f_angle_d0.943
f_chiral_restr0.051
f_bond_d0.008
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3373
Nucleic Acid Atoms382
Solvent Atoms184
Heterogen Atoms36

Software

Software
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
PHASERphasing
PHENIXrefinement