7Z9I

ATAD2 in complex with PepLite-Ala


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 = 79.435α = 90
b = 79.435β = 90
c = 137.648γ = 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
11.561.5499.50.1130.1180.0350.99811.920.941568
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)
11.51.532.9773.1631.0480.40516.8

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-VALUE3DAI1.548.70241518202699.3370.1910.18960.219334.712
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]
-0.044-0.022-0.0440.144
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.301
r_dihedral_angle_4_deg15.911
r_dihedral_angle_3_deg15.556
r_lrange_other11.14
r_lrange_it11.11
r_scangle_it8.704
r_scangle_other8.699
r_scbond_it6.074
r_scbond_other5.26
r_dihedral_angle_1_deg5.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.301
r_dihedral_angle_4_deg15.911
r_dihedral_angle_3_deg15.556
r_lrange_other11.14
r_lrange_it11.11
r_scangle_it8.704
r_scangle_other8.699
r_scbond_it6.074
r_scbond_other5.26
r_dihedral_angle_1_deg5.011
r_mcangle_other4.088
r_mcangle_it4.084
r_mcbond_it2.872
r_mcbond_other2.868
r_angle_refined_deg1.923
r_angle_other_deg1.544
r_symmetry_xyhbond_nbd_refined0.305
r_nbd_other0.249
r_xyhbond_nbd_refined0.24
r_nbd_refined0.216
r_symmetry_nbd_refined0.186
r_symmetry_nbd_other0.182
r_nbtor_refined0.175
r_chiral_restr0.104
r_symmetry_nbtor_other0.08
r_symmetry_xyhbond_nbd_other0.063
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_xyhbond_nbd_other0.007
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 Atoms201
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
xia2data reduction
PHASERphasing