6F5F

Structure of ARTD2/PARP2 WGR domain bound to double strand DNA with 5 nucleotide overhang and 5'phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6F1KPDB ID 6F1K

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.2 M Na-formate 20 % PEG 3350 20 % glycerol
Crystal Properties
Matthews coefficientSolvent content
3.4664.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.15α = 90
b = 87.15β = 90
c = 185.27γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-07-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97949DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
12.982099.80.0690.0750.8815.296.3823275
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.983

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 REPLACEMENTTHROUGHOUTPDB ID 6F1K2.9819.8621936115599.210.230560.228220.2753RANDOM121.612
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]
3.97.42-11.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.531
r_dihedral_angle_3_deg18.868
r_long_range_B_refined16.965
r_long_range_B_other16.964
r_dihedral_angle_4_deg15.417
r_scangle_other14.351
r_mcangle_it13.985
r_mcangle_other13.982
r_scbond_it9.755
r_scbond_other9.755
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.531
r_dihedral_angle_3_deg18.868
r_long_range_B_refined16.965
r_long_range_B_other16.964
r_dihedral_angle_4_deg15.417
r_scangle_other14.351
r_mcangle_it13.985
r_mcangle_other13.982
r_scbond_it9.755
r_scbond_other9.755
r_mcbond_it9.41
r_mcbond_other9.401
r_dihedral_angle_1_deg6.826
r_angle_refined_deg1.778
r_angle_other_deg1.178
r_chiral_restr0.115
r_bond_refined_d0.011
r_gen_planes_refined0.008
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 Atoms3780
Nucleic Acid Atoms1232
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing