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Crystal structure of MLLT1 (ENL) YEATS domain in complexed with benzimidazole-amide derivative 6
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 7.5 293.15 25% PEG 3350, 0.2M sodium chloride, 0.1M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.17 43.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.027 α = 90 b = 49.027 β = 90 c = 131.431 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 1.9 49.03 97.5 0.077 0.09 0.038 0.991 8.7 4.8 13008 31
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 1.9 1.97 94.8 0.418 0.459 0.217 0.913 2.6 4.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6HQ0 1.9 45.94 12297 657 96.98 0.2048 0.2022 0.2148 0.2507 0.2629 RANDOM 39.136
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] -3.29 -3.29 6.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.59 r_dihedral_angle_4_deg 21.084 r_dihedral_angle_3_deg 15.545 r_dihedral_angle_1_deg 8.056 r_angle_refined_deg 1.287 r_angle_other_deg 1.167 r_chiral_restr 0.07 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.59 r_dihedral_angle_4_deg 21.084 r_dihedral_angle_3_deg 15.545 r_dihedral_angle_1_deg 8.056 r_angle_refined_deg 1.287 r_angle_other_deg 1.167 r_chiral_restr 0.07 r_bond_refined_d 0.013 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 87 Heterogen Atoms 71
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing