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Crystal structure of MLLT1 (ENL) YEATS domain in complexed with SGC-iMLLT (compound 92)
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 2.17 43.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.842 α = 90 b = 48.842 β = 90 c = 133.238 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 2.1 48.84 100 0.069 0.027 0.999 13.2 7.8 10098 37.3
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 2.1 2.17 100 0.463 0.185 0.959 3.4 7.6
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 2.1 45.86 9566 473 99.87 0.20296 0.20047 0.2138 0.25204 0.2651 RANDOM 53.746
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] -4.01 -4.01 8.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.15 r_dihedral_angle_4_deg 18.334 r_dihedral_angle_3_deg 14.236 r_long_range_B_refined 8.537 r_long_range_B_other 8.534 r_dihedral_angle_1_deg 7.648 r_scangle_other 4.82 r_scbond_it 3.41 r_scbond_other 3.408 r_mcangle_it 3.171
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.15 r_dihedral_angle_4_deg 18.334 r_dihedral_angle_3_deg 14.236 r_long_range_B_refined 8.537 r_long_range_B_other 8.534 r_dihedral_angle_1_deg 7.648 r_scangle_other 4.82 r_scbond_it 3.41 r_scbond_other 3.408 r_mcangle_it 3.171 r_mcangle_other 3.169 r_mcbond_it 2.224 r_mcbond_other 2.213 r_angle_refined_deg 1.501 r_angle_other_deg 1.231 r_chiral_restr 0.073 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_gen_planes_other 0.002 r_bond_other_d 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 1182 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing