3SE2

Human poly(ADP-ribose) polymerase 14 (PARP14/ARTD8) - catalytic domain in complex with 6(5H)-phenanthridinone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GOYPDB entry 3GOY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529320% PEG3350, 0.2M KSCN, 0.1M Bis-Tris-Propane, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.448.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.372α = 90
b = 82.372β = 90
c = 434.478γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HEmirrors and double crystal monochromator2009-06-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.91841BESSY14.2

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
12.33599.90.1110.16615.713.54041240412
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.361000.7320.4163.59.5

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3GOY2.334.57383913839120211000.210140.207810.25464RANDOM17.994
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]
-0.88-0.44-0.881.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.577
r_dihedral_angle_4_deg20.33
r_dihedral_angle_3_deg15.114
r_dihedral_angle_1_deg6.805
r_scangle_it2.572
r_scbond_it1.551
r_angle_refined_deg1.308
r_mcangle_it1.093
r_angle_other_deg0.866
r_mcbond_it0.578
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.577
r_dihedral_angle_4_deg20.33
r_dihedral_angle_3_deg15.114
r_dihedral_angle_1_deg6.805
r_scangle_it2.572
r_scbond_it1.551
r_angle_refined_deg1.308
r_mcangle_it1.093
r_angle_other_deg0.866
r_mcbond_it0.578
r_mcbond_other0.139
r_chiral_restr0.078
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.004
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6051
Nucleic Acid Atoms
Solvent Atoms151
Heterogen Atoms85

Software

Software
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling