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LSD1/Co-Rest structure with an inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5H6Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 36% Tacsimate
Crystal Properties Matthews coefficient Solvent content 7.14 82.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.51 α = 90 b = 179.44 β = 90 c = 234.41 γ = 90
Symmetry Space Group I 2 2 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 2018-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97918 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.87 76.46 99.4 0.08 13.5 6.8 58422
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.87 2.94 99.7 1.064 7.1
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 5H6Q 2.87 76.46 55234 2828 98.68 0.19028 0.18861 0.22282 0.2334 RANDOM 107.008
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] 11.02 -7.72 -3.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.939 r_dihedral_angle_3_deg 21.188 r_long_range_B_refined 18.993 r_long_range_B_other 18.992 r_dihedral_angle_4_deg 18.758 r_scangle_other 15.844 r_mcangle_it 15.103 r_mcangle_other 15.102 r_scbond_it 10.992 r_scbond_other 10.991
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.939 r_dihedral_angle_3_deg 21.188 r_long_range_B_refined 18.993 r_long_range_B_other 18.992 r_dihedral_angle_4_deg 18.758 r_scangle_other 15.844 r_mcangle_it 15.103 r_mcangle_other 15.102 r_scbond_it 10.992 r_scbond_other 10.991 r_mcbond_it 10.925 r_mcbond_other 10.919 r_dihedral_angle_1_deg 8.328 r_angle_refined_deg 1.909 r_angle_other_deg 1.274 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 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 6253 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 222
Software Software Software Name Purpose REFMAC refinement xia2 data scaling PHASER phasing PDB_EXTRACT data extraction xia2 data reduction