7QWO

ATAD2 in complex with FragLite6


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.1M BisTris pH 6-7, 1.7-2.1M Ammonium sulphate

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.777α = 90
b = 79.777β = 90
c = 135.692γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-07-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.976DiamondI04-1

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
11.569.091000.1360.1430.0440.999101941617
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5336.60817.1090.3739

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-VALUE3DAI1.561.64441542207499.9330.2410.23920.272541.941
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]
-1.488-0.744-1.4884.826
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.013
r_lrange_it25.33
r_lrange_other25.321
r_dihedral_angle_3_deg14.19
r_dihedral_angle_4_deg13.158
r_scangle_other8.105
r_scangle_it8.098
r_mcangle_other5.55
r_mcangle_it5.547
r_dihedral_angle_1_deg5.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.013
r_lrange_it25.33
r_lrange_other25.321
r_dihedral_angle_3_deg14.19
r_dihedral_angle_4_deg13.158
r_scangle_other8.105
r_scangle_it8.098
r_mcangle_other5.55
r_mcangle_it5.547
r_dihedral_angle_1_deg5.44
r_scbond_it5.279
r_scbond_other5.272
r_mcbond_it4.018
r_mcbond_other4.007
r_angle_refined_deg1.686
r_angle_other_deg1.387
r_symmetry_nbd_refined0.878
r_nbd_other0.45
r_symmetry_xyhbond_nbd_refined0.273
r_nbd_refined0.235
r_xyhbond_nbd_refined0.203
r_symmetry_nbd_other0.191
r_nbtor_refined0.173
r_chiral_restr0.088
r_symmetry_nbtor_other0.083
r_xyhbond_nbd_other0.031
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1084
Nucleic Acid Atoms
Solvent Atoms138
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
xia2data reduction
xia2data scaling
PHASERphasing