7PPX

ATAD2 in complex with FragLite3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DAI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1M HEPES pH 7.0, 2.4 AmSO4, ATAD2~5 mg mL-1.

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.205α = 90
b = 79.205β = 90
c = 137.91γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.97959DiamondI04-1

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
11.3568.9699.70.0550.0580.017122.919.856615
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)
11.351.373.94.3171.8130.20410.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3DAI1.3568.68856534293699.6070.2120.21080.230632.546
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]
0.0240.0120.024-0.077
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.235
r_dihedral_angle_4_deg18.919
r_dihedral_angle_3_deg17.038
r_lrange_it11.505
r_scangle_it8.356
r_scbond_it5.761
r_dihedral_angle_1_deg4.558
r_mcangle_it3.992
r_mcbond_it2.817
r_angle_refined_deg2.247
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.235
r_dihedral_angle_4_deg18.919
r_dihedral_angle_3_deg17.038
r_lrange_it11.505
r_scangle_it8.356
r_scbond_it5.761
r_dihedral_angle_1_deg4.558
r_mcangle_it3.992
r_mcbond_it2.817
r_angle_refined_deg2.247
r_nbtor_refined0.319
r_symmetry_xyhbond_nbd_refined0.234
r_nbd_refined0.227
r_xyhbond_nbd_refined0.19
r_symmetry_nbd_refined0.177
r_chiral_restr0.137
r_bond_refined_d0.016
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1084
Nucleic Acid Atoms
Solvent Atoms163
Heterogen Atoms65

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
pointlessdata scaling
DIALSdata collection
DIMPLEphasing
Cootmodel building
DIALSdata reduction