7B10

Crystal structure of MLLT1 YEATS domain T1 mutant in complex with benzimidazole-amide based compound 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6T1L 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.529325% w/v PEG 3350, 0.1M Bis-Tris, pH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.0840.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.111α = 90
b = 39.357β = 125.58
c = 53.111γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-03-07MSINGLE 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
11.9243.299.20.0790.0920.0460.9967.93.811770
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)
11.921.9999.80.6450.7510.3790.8033.9

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 REPLACEMENTTHROUGHOUT6T1L1.9243.21125449198.840.17540.17390.2094RANDOM39.477
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]
-2.52-0.211.470.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.332
r_dihedral_angle_4_deg22.661
r_dihedral_angle_3_deg14.33
r_dihedral_angle_1_deg6.897
r_angle_refined_deg1.572
r_angle_other_deg1.232
r_chiral_restr0.076
r_bond_refined_d0.015
r_gen_planes_refined0.012
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.332
r_dihedral_angle_4_deg22.661
r_dihedral_angle_3_deg14.33
r_dihedral_angle_1_deg6.897
r_angle_refined_deg1.572
r_angle_other_deg1.232
r_chiral_restr0.076
r_bond_refined_d0.015
r_gen_planes_refined0.012
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1181
Nucleic Acid Atoms
Solvent Atoms63
Heterogen Atoms98

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing