7Z9O

ATAD2 in complex with PepLite-Tyr


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 = 79.297α = 90
b = 79.297β = 90
c = 138.39γ = 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 I04-10.9762DiamondI04-1

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
11.4761.5299.40.0880.0930.0270.99916.820.544189
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)
11.471.54.8615.2551.9030.25413.4

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-VALUE3DAI1.4761.5244128221399.2730.2020.2010.217635.912
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]
0.1240.0620.124-0.401
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.851
r_dihedral_angle_4_deg15.078
r_dihedral_angle_3_deg14.654
r_lrange_it11.23
r_scangle_it8.455
r_scbond_it5.982
r_dihedral_angle_1_deg4.427
r_mcangle_it4.201
r_mcbond_it2.904
r_angle_refined_deg2.393
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.851
r_dihedral_angle_4_deg15.078
r_dihedral_angle_3_deg14.654
r_lrange_it11.23
r_scangle_it8.455
r_scbond_it5.982
r_dihedral_angle_1_deg4.427
r_mcangle_it4.201
r_mcbond_it2.904
r_angle_refined_deg2.393
r_symmetry_nbd_refined0.474
r_symmetry_xyhbond_nbd_refined0.436
r_nbtor_refined0.32
r_xyhbond_nbd_refined0.247
r_nbd_refined0.226
r_chiral_restr0.139
r_bond_refined_d0.025
r_gen_planes_refined0.016
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1084
Nucleic Acid Atoms
Solvent Atoms180
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
xia2data reduction
PHASERphasing