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Crystal structure of MLLT1 (ENL) YEATS domain in complexed with compound 94
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5J9S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 25% PEG3350, 0.2M ammonium sulfate, 0.1M bis-tris pH 5.5 or 25% PEG Smear Medi-um, 0.1M citrate pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.16 43.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.754 α = 90 b = 48.754 β = 90 c = 132.858 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 2018-09-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 45.77 100 0.059 0.02 0.999 17.6 10 15693 28.1
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) Redundancy Number Unique Reflections (All) 1 1.8 1.84 100 0.774 0.263 0.884 2.6 10.3
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 5J9S 1.8 45.77 14848 778 99.96 0.19738 0.19558 0.209 0.23045 0.2374 RANDOM 33.919
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] -1.62 -1.62 3.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.805 r_dihedral_angle_4_deg 17.581 r_dihedral_angle_3_deg 13.595 r_dihedral_angle_1_deg 6.786 r_long_range_B_refined 5.943 r_long_range_B_other 5.941 r_scangle_other 2.795 r_mcangle_it 2.143 r_mcangle_other 2.141 r_scbond_it 1.755
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.805 r_dihedral_angle_4_deg 17.581 r_dihedral_angle_3_deg 13.595 r_dihedral_angle_1_deg 6.786 r_long_range_B_refined 5.943 r_long_range_B_other 5.941 r_scangle_other 2.795 r_mcangle_it 2.143 r_mcangle_other 2.141 r_scbond_it 1.755 r_scbond_other 1.753 r_angle_refined_deg 1.522 r_mcbond_it 1.279 r_mcbond_other 1.279 r_angle_other_deg 1.278 r_chiral_restr 0.074 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1186 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing