7QZM

ATAD2 in complex with FragLite28


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 = 79.068α = 90
b = 79.068β = 90
c = 137.07γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-11-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.911DiamondI04-1

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
11.4568.541000.0580.0590.0130.99931.73845657
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)
11.451.475.4765.6521.390.36431.3

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-VALUE3DAI1.4568.5445582231799.9710.2090.20770.242334.054
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]
-0.171-0.085-0.1710.555
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.891
r_dihedral_angle_4_deg15.653
r_dihedral_angle_3_deg15.192
r_lrange_it9.132
r_lrange_other9.129
r_scangle_it7.128
r_scangle_other7.124
r_scbond_it5.02
r_scbond_other5.016
r_dihedral_angle_1_deg4.612
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.891
r_dihedral_angle_4_deg15.653
r_dihedral_angle_3_deg15.192
r_lrange_it9.132
r_lrange_other9.129
r_scangle_it7.128
r_scangle_other7.124
r_scbond_it5.02
r_scbond_other5.016
r_dihedral_angle_1_deg4.612
r_mcangle_it4.24
r_mcangle_other4.237
r_mcbond_it3.029
r_mcbond_other3.026
r_angle_refined_deg2.092
r_angle_other_deg1.508
r_nbd_refined0.23
r_symmetry_nbd_refined0.212
r_nbd_other0.212
r_xyhbond_nbd_refined0.202
r_symmetry_xyhbond_nbd_refined0.196
r_symmetry_nbd_other0.183
r_nbtor_refined0.182
r_chiral_restr0.099
r_symmetry_nbtor_other0.082
r_xyhbond_nbd_other0.066
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 Atoms141
Heterogen Atoms66

Software

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