7QYL

ATAD2 in complex with FragLite23


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 Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.521α = 90
b = 79.521β = 90
c = 137.408γ = 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
11.4468.8799.90.0580.060.018120.519.647120
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)
11.441.473.994.4131.8680.33710.5

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-VALUE3DAI1.4468.8747049231699.790.2210.220.243733.702
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]
-0.477-0.238-0.4771.547
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.904
r_dihedral_angle_3_deg15.021
r_dihedral_angle_4_deg12.43
r_lrange_it9.014
r_lrange_other8.992
r_scangle_other7.131
r_scangle_it7.112
r_scbond_it4.967
r_scbond_other4.962
r_dihedral_angle_1_deg4.496
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.904
r_dihedral_angle_3_deg15.021
r_dihedral_angle_4_deg12.43
r_lrange_it9.014
r_lrange_other8.992
r_scangle_other7.131
r_scangle_it7.112
r_scbond_it4.967
r_scbond_other4.962
r_dihedral_angle_1_deg4.496
r_mcangle_other4.078
r_mcangle_it4.076
r_mcbond_it2.904
r_mcbond_other2.899
r_angle_refined_deg2.121
r_angle_other_deg1.487
r_xyhbond_nbd_refined0.235
r_symmetry_xyhbond_nbd_refined0.233
r_symmetry_xyhbond_nbd_other0.232
r_nbd_refined0.231
r_nbd_other0.197
r_symmetry_nbd_other0.178
r_nbtor_refined0.178
r_symmetry_nbd_refined0.172
r_chiral_restr0.105
r_xyhbond_nbd_other0.093
r_symmetry_nbtor_other0.083
r_bond_refined_d0.015
r_gen_planes_refined0.011
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 Atoms127
Heterogen Atoms53

Software

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