7Z9J

ATAD2 in complex with PepLite-Gly


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 Properties
Matthews coefficientSolvent content
4.169.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.772α = 90
b = 79.772β = 90
c = 137.872γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-09-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9116DiamondI04-1

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
11.948.81000.2590.2660.0580.99914.338.921195
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)
11.91.945.0465.1741.1420.72638.5

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-VALUE3DAI1.948.821134102699.9860.1910.18910.221336.854
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]
-0.24-0.12-0.240.779
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.575
r_dihedral_angle_4_deg18.211
r_dihedral_angle_3_deg15.872
r_lrange_it9.848
r_scangle_it7.397
r_scbond_it5.634
r_dihedral_angle_1_deg5.18
r_mcangle_it4.207
r_mcbond_it3.188
r_angle_refined_deg1.867
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.575
r_dihedral_angle_4_deg18.211
r_dihedral_angle_3_deg15.872
r_lrange_it9.848
r_scangle_it7.397
r_scbond_it5.634
r_dihedral_angle_1_deg5.18
r_mcangle_it4.207
r_mcbond_it3.188
r_angle_refined_deg1.867
r_symmetry_nbd_refined0.409
r_nbtor_refined0.315
r_nbd_refined0.229
r_xyhbond_nbd_refined0.213
r_symmetry_xyhbond_nbd_refined0.192
r_chiral_restr0.119
r_bond_refined_d0.013
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1084
Nucleic Acid Atoms
Solvent Atoms180
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
xia2data reduction
PHASERphasing