7QX1

ATAD2 in complex with FragLite7


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 = 79.599α = 90
b = 79.599β = 90
c = 137.348γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.979DiamondI04-1

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
11.4968.931000.0680.0720.02211918.842789
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)
11.491.522.5052.8151.2470.5468.4

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-VALUE3DAI1.4968.9342712218899.9320.2070.20460.242434.025
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]
-0.685-0.342-0.6852.221
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.983
r_lrange_it16.628
r_lrange_other16.622
r_dihedral_angle_3_deg13.259
r_dihedral_angle_4_deg12.019
r_scangle_other11.265
r_scangle_it11.235
r_scbond_other7.944
r_scbond_it7.926
r_dihedral_angle_1_deg4.796
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.983
r_lrange_it16.628
r_lrange_other16.622
r_dihedral_angle_3_deg13.259
r_dihedral_angle_4_deg12.019
r_scangle_other11.265
r_scangle_it11.235
r_scbond_other7.944
r_scbond_it7.926
r_dihedral_angle_1_deg4.796
r_mcangle_other3.982
r_mcangle_it3.979
r_mcbond_it2.899
r_mcbond_other2.894
r_angle_refined_deg1.941
r_angle_other_deg1.51
r_symmetry_nbd_refined0.34
r_nbd_other0.283
r_symmetry_xyhbond_nbd_refined0.265
r_nbd_refined0.224
r_xyhbond_nbd_refined0.207
r_symmetry_nbd_other0.183
r_nbtor_refined0.178
r_xyhbond_nbd_other0.104
r_chiral_restr0.096
r_symmetry_nbtor_other0.082
r_bond_refined_d0.014
r_gen_planes_refined0.01
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 Atoms161
Heterogen Atoms47

Software

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