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Crystal structure of MLLT1 (ENL) YEATS domain in complexed with benzimidazole-amide derivative 5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HQ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293.15 25% PEG 3350, 0.2M sodium chloride, 0.1M bis-tris pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.18 43.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.014 α = 90 b = 49.014 β = 90 c = 132.425 γ = 90
Symmetry Space Group P 43 21 2
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 2018-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0000 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 1.95 49.01 100 0.082 0.092 0.033 0.997 9.8 7.1 12512 33.6
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 1.95 2.02 100 0.735 0.84 0.304 0.83 2.2 7.4
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 6HQ0 1.95 45.97 11870 595 99.86 0.2116 0.2088 0.266 0.2844 RANDOM 42.801
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] -2.27 -2.27 4.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.717 r_dihedral_angle_4_deg 20.315 r_dihedral_angle_3_deg 14.272 r_dihedral_angle_1_deg 8.024 r_angle_refined_deg 1.199 r_angle_other_deg 1.102 r_chiral_restr 0.064 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.717 r_dihedral_angle_4_deg 20.315 r_dihedral_angle_3_deg 14.272 r_dihedral_angle_1_deg 8.024 r_angle_refined_deg 1.199 r_angle_other_deg 1.102 r_chiral_restr 0.064 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1172 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 54
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing