7Z9U

ATAD2 in complex with Acetyl-Lys


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
4.0269.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.029α = 90
b = 79.029β = 90
c = 137.875γ = 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 I04-10.91162DiamondI04-1

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
11.7648.571000.150.1530.033119.639.226026
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.761.7910.6372.2950.32740.4

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-VALUE3DAI1.7648.5725962134599.9580.2060.20470.227142.31
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]
-0.419-0.209-0.4191.359
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.459
r_dihedral_angle_4_deg16.635
r_dihedral_angle_3_deg15.665
r_lrange_it11.515
r_scangle_it9.461
r_scbond_it6.64
r_dihedral_angle_1_deg5.51
r_mcangle_it5.477
r_mcbond_it4.142
r_angle_refined_deg2.046
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.459
r_dihedral_angle_4_deg16.635
r_dihedral_angle_3_deg15.665
r_lrange_it11.515
r_scangle_it9.461
r_scbond_it6.64
r_dihedral_angle_1_deg5.51
r_mcangle_it5.477
r_mcbond_it4.142
r_angle_refined_deg2.046
r_symmetry_xyhbond_nbd_refined0.475
r_nbtor_refined0.322
r_nbd_refined0.228
r_xyhbond_nbd_refined0.194
r_symmetry_nbd_refined0.16
r_chiral_restr0.135
r_bond_refined_d0.013
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1084
Nucleic Acid Atoms
Solvent Atoms113
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
xia2data reduction
PHASERphasing