6BRX

Crystal Structure of Human DNA polymerase kappa in complex with DNA containing the major cisplatin lesion


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP295.1515-20% PEG400 and 0.1-0.2 M ammonium iodide (NH4I)
Crystal Properties
Matthews coefficientSolvent content
2.5852.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.69α = 90
b = 129.06β = 90
c = 168.088γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002014-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97949CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.848.4799.60.0930.9969.74.436493
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.950.5240.82822702

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT2.848.4734925140599.370.215630.213590.26895RANDOM73.975
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]
10.33-6.28-4.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.176
r_dihedral_angle_4_deg20.953
r_dihedral_angle_3_deg16.443
r_long_range_B_refined7.956
r_long_range_B_other7.941
r_dihedral_angle_1_deg5.161
r_mcangle_it4.862
r_mcangle_other4.861
r_scangle_other4.601
r_mcbond_it2.894
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.176
r_dihedral_angle_4_deg20.953
r_dihedral_angle_3_deg16.443
r_long_range_B_refined7.956
r_long_range_B_other7.941
r_dihedral_angle_1_deg5.161
r_mcangle_it4.862
r_mcangle_other4.861
r_scangle_other4.601
r_mcbond_it2.894
r_mcbond_other2.894
r_scbond_it2.747
r_scbond_other2.747
r_angle_refined_deg1.22
r_angle_other_deg1.188
r_chiral_restr0.069
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.004
r_gen_planes_other0.003
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 Atoms6695
Nucleic Acid Atoms896
Solvent Atoms230
Heterogen Atoms81

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
REFMACphasing