5QHY

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of human PARP14 Macrodomain 3 in complex with FMOPL000462a


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.427780 mM KBr, 30 % PEG2kMME
Crystal Properties
Matthews coefficientSolvent content
238.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.341α = 90
b = 41.653β = 90
c = 111.018γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-03-04SINGLE 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
11.1729.2990.0430.0470.0190.99916.55.254380
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)
11.171.288.20.4810.6110.370.8422.23529

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 SYNTHESISTHROUGHOUT4ABL1.1755.5751501278198.850.15170.150.1863RANDOM19.117
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]
1.32-0.31-1.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.255
r_sphericity_free26.327
r_dihedral_angle_4_deg16.684
r_dihedral_angle_3_deg12.389
r_sphericity_bonded10.247
r_dihedral_angle_1_deg5.69
r_mcangle_it2.103
r_rigid_bond_restr1.968
r_mcbond_it1.596
r_angle_refined_deg1.595
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.255
r_sphericity_free26.327
r_dihedral_angle_4_deg16.684
r_dihedral_angle_3_deg12.389
r_sphericity_bonded10.247
r_dihedral_angle_1_deg5.69
r_mcangle_it2.103
r_rigid_bond_restr1.968
r_mcbond_it1.596
r_angle_refined_deg1.595
r_mcbond_other1.585
r_angle_other_deg0.997
r_chiral_restr0.101
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1380
Nucleic Acid Atoms
Solvent Atoms199
Heterogen Atoms19

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing