4EEY

Crystal structure of human DNA polymerase eta in ternary complex with a cisplatin DNA adduct


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MR2PDB ENTRY 3MR2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529315-35% PEG1500, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0941.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.5α = 90
b = 98.5β = 90
c = 82.603γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-09-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.0722NSLSX25

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.325099.850.10816.96.219767197341
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)
12.322.3899.90.4623.85.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3MR22.3249.251976418206152899.850.182470.182470.178340.23253RANDOM34.458
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]
-0.4-0.2-0.40.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.332
r_dihedral_angle_4_deg17.095
r_dihedral_angle_3_deg14.103
r_dihedral_angle_1_deg5.028
r_scangle_it1.618
r_angle_refined_deg1.134
r_scbond_it1.079
r_mcangle_it0.605
r_mcbond_it0.299
r_chiral_restr0.069
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.332
r_dihedral_angle_4_deg17.095
r_dihedral_angle_3_deg14.103
r_dihedral_angle_1_deg5.028
r_scangle_it1.618
r_angle_refined_deg1.134
r_scbond_it1.079
r_mcangle_it0.605
r_mcbond_it0.299
r_chiral_restr0.069
r_bond_refined_d0.008
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3255
Nucleic Acid Atoms388
Solvent Atoms116
Heterogen Atoms32

Software

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