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Crystal structure of MLLT1 YEATS domain T1 mutant in complex with benzimidazole-amide based compound 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6T1L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 25% w/v PEG 3350, 0.1M Bis-Tris, pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.08 40.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.111 α = 90 b = 39.357 β = 125.58 c = 53.111 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2020-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000 SLS X06SA
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.92 43.2 99.2 0.079 0.092 0.046 0.996 7.9 3.8 11770
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) Redundancy Number Unique Reflections (All) 1 1.92 1.99 99.8 0.645 0.751 0.379 0.803 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6T1L 1.92 43.2 11254 491 98.84 0.1754 0.1739 0.2094 0.2308 RANDOM 39.477
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 -0.21 1.47 0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.332 r_dihedral_angle_4_deg 22.661 r_dihedral_angle_3_deg 14.33 r_dihedral_angle_1_deg 6.897 r_angle_refined_deg 1.572 r_angle_other_deg 1.232 r_chiral_restr 0.076 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.332 r_dihedral_angle_4_deg 22.661 r_dihedral_angle_3_deg 14.33 r_dihedral_angle_1_deg 6.897 r_angle_refined_deg 1.572 r_angle_other_deg 1.232 r_chiral_restr 0.076 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1181 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 98
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing