7QUK

ATAD2 in complex with FragLite1


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 = 79.298α = 90
b = 79.298β = 90
c = 137.846γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-07-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.97DiamondI04-1

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
11.4761.471000.080.0840.0250.99916.620.144319
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)
11.471.53.8384.1721.6130.37512.4

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-VALUE3DAI1.4761.4744243217199.9340.2030.2020.230431.643
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]
0.0480.0240.048-0.155
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.554
r_lrange_it19.327
r_lrange_other19.321
r_dihedral_angle_3_deg13.306
r_dihedral_angle_4_deg10.776
r_scangle_other8.686
r_scangle_it8.662
r_scbond_it4.825
r_scbond_other4.813
r_dihedral_angle_1_deg4.422
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.554
r_lrange_it19.327
r_lrange_other19.321
r_dihedral_angle_3_deg13.306
r_dihedral_angle_4_deg10.776
r_scangle_other8.686
r_scangle_it8.662
r_scbond_it4.825
r_scbond_other4.813
r_dihedral_angle_1_deg4.422
r_mcangle_other4.005
r_mcangle_it3.995
r_mcbond_it2.885
r_mcbond_other2.87
r_angle_refined_deg2.109
r_angle_other_deg1.563
r_symmetry_nbd_refined0.699
r_nbd_other0.399
r_nbd_refined0.259
r_xyhbond_nbd_refined0.231
r_symmetry_nbd_other0.194
r_nbtor_refined0.179
r_symmetry_xyhbond_nbd_refined0.177
r_chiral_restr0.103
r_xyhbond_nbd_other0.097
r_symmetry_nbtor_other0.083
r_symmetry_xyhbond_nbd_other0.083
r_bond_refined_d0.016
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 Atoms140
Heterogen Atoms21

Software

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