5QHU

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of human PARP14 Macrodomain 3 in complex with FMSOA000341b


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.427780 mM KBr, 30 % PEG2kMME
Crystal Properties
Matthews coefficientSolvent content
1.9938.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.32α = 90
b = 41.48β = 90
c = 110.73γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-02-10SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92819DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.0555.3782.80.0350.0380.0160.99920.84.861811
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.051.0814.30.3340.4620.3160.6971.1772

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT4ABL1.0555.4358583314982.780.14270.14160.1656RANDOM14.12
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]
0.73-0.31-0.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.279
r_sphericity_free27.9
r_dihedral_angle_4_deg22.564
r_dihedral_angle_3_deg11.671
r_sphericity_bonded7.524
r_dihedral_angle_1_deg5.654
r_angle_refined_deg1.515
r_mcangle_it1.479
r_rigid_bond_restr1.333
r_mcbond_it1.085
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.279
r_sphericity_free27.9
r_dihedral_angle_4_deg22.564
r_dihedral_angle_3_deg11.671
r_sphericity_bonded7.524
r_dihedral_angle_1_deg5.654
r_angle_refined_deg1.515
r_mcangle_it1.479
r_rigid_bond_restr1.333
r_mcbond_it1.085
r_mcbond_other1.079
r_angle_other_deg1.003
r_chiral_restr0.098
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1380
Nucleic Acid Atoms
Solvent Atoms190
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing