8SDO

ATAD2 bromodomain in complex with "oncohistone" mutation H4S1CK5ac (res 1-15) ligand


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DAI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2772.4 M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, pH 6.4
Crystal Properties
Matthews coefficientSolvent content
3.0259.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.941α = 90
b = 53.941β = 90
c = 159.522γ = 90
Symmetry
Space GroupP 43 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293CMOSRDI CMOS_8M2021-04-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.21.0722ALS4.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.0127.4699.510.99918.9113.41648043.36
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.012.0820.372

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.0127.461.331641176299.580.20210.20070.230556.87
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d26.9932
f_angle_d0.8904
f_chiral_restr0.0503
f_plane_restr0.0071
f_bond_d0.0064
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1128
Nucleic Acid Atoms
Solvent Atoms168
Heterogen Atoms

Software

Software
Software NamePurpose
PHENIXrefinement
Cootmodel building
PHASERphasing
XDSdata reduction
XDSdata scaling