7QZY

ATAD2 in complex with FragLite29


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.1M BisTris pH 6-7, 1.7-2.1M Ammonium sulphate
Crystal Properties
Matthews coefficientSolvent content
3.9969.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.16α = 90
b = 79.16β = 90
c = 136.456γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-06-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.915DiamondI04-1

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
11.9368.551000.1420.1490.0450.9991319.719756
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)
11.931.982.7842.9450.9550.6617.6

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-VALUE3DAI1.9368.5519675100399.8530.20.19730.245340.093
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]
-0.103-0.051-0.1030.333
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.976
r_dihedral_angle_4_deg17.396
r_dihedral_angle_3_deg15.367
r_lrange_it11.892
r_lrange_other11.888
r_scangle_it8.336
r_scangle_other8.331
r_scbond_it5.634
r_scbond_other5.634
r_mcangle_it5.252
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.976
r_dihedral_angle_4_deg17.396
r_dihedral_angle_3_deg15.367
r_lrange_it11.892
r_lrange_other11.888
r_scangle_it8.336
r_scangle_other8.331
r_scbond_it5.634
r_scbond_other5.634
r_mcangle_it5.252
r_mcangle_other5.248
r_dihedral_angle_1_deg5.175
r_mcbond_other4.039
r_mcbond_it4.035
r_angle_refined_deg1.787
r_angle_other_deg1.429
r_symmetry_nbd_refined0.398
r_nbd_other0.232
r_xyhbond_nbd_refined0.224
r_symmetry_xyhbond_nbd_refined0.222
r_nbd_refined0.218
r_symmetry_nbd_other0.191
r_nbtor_refined0.175
r_chiral_restr0.098
r_symmetry_nbtor_other0.08
r_symmetry_xyhbond_nbd_other0.04
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1084
Nucleic Acid Atoms
Solvent Atoms118
Heterogen Atoms63

Software

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