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Crystal structure of Lysine Specific Demethylase 1 (LSD1) with TAS1440
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YJB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 293 100mM ADA pH6.5, 1.22M Na/K Tartrate
Crystal Properties Matthews coefficient Solvent content 7.18 82.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.772 α = 90 b = 179.115 β = 90 c = 235.029 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 4M 2020-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.0800 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 3.2 49.13 100 0.11 0.119 0.998 13.3 6.9 42711
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.37 100 0.877 0.945 0.853 2.4 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.2 49.13 40566 2145 99.94 0.19451 0.19266 0.198 0.23025 0.2298 RANDOM 90.082
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] -0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.742 r_dihedral_angle_4_deg 22.399 r_dihedral_angle_3_deg 21.082 r_long_range_B_refined 17.426 r_long_range_B_other 17.425 r_scangle_other 14.944 r_mcangle_it 13.894 r_mcangle_other 13.892 r_scbond_it 10.231 r_scbond_other 10.229
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.742 r_dihedral_angle_4_deg 22.399 r_dihedral_angle_3_deg 21.082 r_long_range_B_refined 17.426 r_long_range_B_other 17.425 r_scangle_other 14.944 r_mcangle_it 13.894 r_mcangle_other 13.892 r_scbond_it 10.231 r_scbond_other 10.229 r_mcbond_it 9.458 r_mcbond_other 9.45 r_dihedral_angle_1_deg 8.889 r_angle_refined_deg 2.323 r_angle_other_deg 1.3 r_chiral_restr 0.111 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.003 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 5856 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement