7TY3

Crystal Structure of SETD2 Bound to an Indole-based Inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherSETD2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1 M Potassium thiocyanate, 0.1 M Tris pH 7.5, 18% w/v PEG 2000 MME
Crystal Properties
Matthews coefficientSolvent content
2.3647.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.092α = 90
b = 76.702β = 90
c = 75.461γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2019-10-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL45XU1.00SPring-8BL45XU

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
12.343.1395.80.9985.84.112603
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.380.824

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTSETD22.343.131260368095.10.21630.21360.2695RANDOM64.88
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]
3.71-6.312.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.623
r_dihedral_angle_4_deg19.645
r_dihedral_angle_3_deg15.587
r_dihedral_angle_1_deg6.633
r_angle_refined_deg1.405
r_angle_other_deg1.142
r_chiral_restr0.052
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.623
r_dihedral_angle_4_deg19.645
r_dihedral_angle_3_deg15.587
r_dihedral_angle_1_deg6.633
r_angle_refined_deg1.405
r_angle_other_deg1.142
r_chiral_restr0.052
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1920
Nucleic Acid Atoms
Solvent Atoms25
Heterogen Atoms63

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction