9QYD | pdb_00009qyd

PARP9 Macro domain 1, Free form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFoldAF-Q8IXQ6-F1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72982.4M Sodium malonate, 4% PPG P400
Crystal Properties
Matthews coefficientSolvent content
238.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.701α = 90
b = 63.847β = 90
c = 69.53γ = 90
Symmetry
Space GroupP 21 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2024-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.9655ESRFMASSIF-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.9147.031000.9989.46.314316
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.911.961000.535

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.9147.031353675399.860.189310.186790.19530.235070.2133RANDOM30.821
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]
-0.940.270.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.406
r_dihedral_angle_2_deg8.581
r_long_range_B_refined7.537
r_long_range_B_other7.509
r_dihedral_angle_1_deg6.997
r_scangle_other5.394
r_scbond_it3.524
r_scbond_other3.522
r_mcangle_it3.284
r_mcangle_other3.283
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.406
r_dihedral_angle_2_deg8.581
r_long_range_B_refined7.537
r_long_range_B_other7.509
r_dihedral_angle_1_deg6.997
r_scangle_other5.394
r_scbond_it3.524
r_scbond_other3.522
r_mcangle_it3.284
r_mcangle_other3.283
r_mcbond_it2.233
r_mcbond_other2.231
r_angle_refined_deg1.539
r_angle_other_deg0.523
r_chiral_restr0.071
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms1496
Nucleic Acid Atoms
Solvent Atoms70
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing