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Crystal structure of Lysine Specific Demethylase 1 (LSD1) with CC-90011
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZMU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 1.3M Na Tartrate
Crystal Properties Matthews coefficient Solvent content 7.24 83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.655 α = 90 b = 178.51 β = 90 c = 236.049 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 80 CCD ADSC QUANTUM 210 2017-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17B1 1.0 SSRF BL17B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.93 50 100 0.077 0.083 0.032 6.8 6.6 55358
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 2.93 3.03 99.9 0.902 0.98 0.381 0.83 6.5
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 3zmu 2.93 49.27 52530 2723 99.36 0.1936 0.1914 0.1998 0.2352 0.2383 RANDOM 89.562
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] 9.99 -5.79 -4.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.426 r_dihedral_angle_4_deg 22.102 r_dihedral_angle_3_deg 20.663 r_dihedral_angle_1_deg 9.365 r_angle_refined_deg 1.941 r_angle_other_deg 1.316 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.426 r_dihedral_angle_4_deg 22.102 r_dihedral_angle_3_deg 20.663 r_dihedral_angle_1_deg 9.365 r_angle_refined_deg 1.941 r_angle_other_deg 1.316 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6115 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing