7Z9N

ATAD2 in complex with PepLite-Val


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 = 79.158α = 90
b = 79.158β = 90
c = 138.043γ = 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
11.3461.498.40.0470.0490.0150.99827.918.256991
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)
11.341.361.7342.0491.0680.3756

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-VALUE3DAI1.3448.68656917282298.1410.2090.20780.22730.216
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]
0.1290.0650.129-0.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.7
r_dihedral_angle_4_deg15.868
r_dihedral_angle_3_deg13.546
r_lrange_it9.529
r_scangle_it7.993
r_scbond_it5.727
r_dihedral_angle_1_deg4.606
r_mcangle_it3.622
r_angle_refined_deg2.601
r_mcbond_it2.447
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.7
r_dihedral_angle_4_deg15.868
r_dihedral_angle_3_deg13.546
r_lrange_it9.529
r_scangle_it7.993
r_scbond_it5.727
r_dihedral_angle_1_deg4.606
r_mcangle_it3.622
r_angle_refined_deg2.601
r_mcbond_it2.447
r_symmetry_xyhbond_nbd_refined0.393
r_nbtor_refined0.325
r_nbd_refined0.226
r_xyhbond_nbd_refined0.217
r_symmetry_nbd_refined0.198
r_chiral_restr0.129
r_bond_refined_d0.023
r_gen_planes_refined0.016
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1084
Nucleic Acid Atoms
Solvent Atoms183
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
xia2data reduction
PHASERphasing