7B0T

Crystal structure of MLLT1 YEATS domain T3 mutant in complex with benzimidazole-amide based compound 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6T1J 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP629328% PEG 3350, 0.2M NaOAc, 0.1M Bis-Tris, pH6.0
Crystal Properties
Matthews coefficientSolvent content
2.1743.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.739α = 90
b = 48.739β = 90
c = 131.995γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.000SLSX06SA

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
12.0548.741000.0940.0990.0310.99911.59.610697
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.111001.1690.3780.85810.1

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 REPLACEMENTTHROUGHOUT6t1j2.0545.721014249699.950.22080.2180.2756RANDOM56.281
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]
-2.7-2.75.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_4_deg21.987
r_dihedral_angle_2_deg20.477
r_dihedral_angle_3_deg16.091
r_dihedral_angle_1_deg7.861
r_angle_refined_deg1.313
r_angle_other_deg1.177
r_chiral_restr0.064
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_4_deg21.987
r_dihedral_angle_2_deg20.477
r_dihedral_angle_3_deg16.091
r_dihedral_angle_1_deg7.861
r_angle_refined_deg1.313
r_angle_other_deg1.177
r_chiral_restr0.064
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1123
Nucleic Acid Atoms
Solvent Atoms13
Heterogen Atoms47

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MLPHAREphasing