7Z9H

ATAD2 in complex with PepLite-Asp


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 = 79.145α = 90
b = 79.145β = 90
c = 137.536γ = 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
11.3468.5499.30.0470.050.015124.917.357366
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)
11.341.361.5641.8981.0530.2965.2

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-VALUE3DAI1.3468.5457288298199.1950.2110.20990.226931.198
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]
0.1590.080.159-0.517
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.089
r_dihedral_angle_3_deg14.49
r_dihedral_angle_4_deg14.009
r_lrange_it11.934
r_scangle_it8.137
r_scbond_it5.628
r_dihedral_angle_1_deg4.367
r_mcangle_it3.711
r_mcbond_it2.529
r_angle_refined_deg2.264
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.089
r_dihedral_angle_3_deg14.49
r_dihedral_angle_4_deg14.009
r_lrange_it11.934
r_scangle_it8.137
r_scbond_it5.628
r_dihedral_angle_1_deg4.367
r_mcangle_it3.711
r_mcbond_it2.529
r_angle_refined_deg2.264
r_nbtor_refined0.322
r_symmetry_xyhbond_nbd_refined0.29
r_nbd_refined0.238
r_xyhbond_nbd_refined0.217
r_symmetry_nbd_refined0.19
r_chiral_restr0.127
r_bond_refined_d0.014
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1084
Nucleic Acid Atoms
Solvent Atoms180
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
xia2data reduction
PHASERphasing