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Crystal structure of Lysine Specific Demethylase 1 (LSD1) with TAK-418 distomer, FAD-adduct
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z5U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1 M imidazole-HCl (pH 6.5), 10% PEG 3350, 10% 2-methyl-2,4-pentanediol and 50 mM ammonium formate
Crystal Properties Matthews coefficient Solvent content 3.63 66.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.727 α = 90 b = 184.727 β = 90 c = 108.937 γ = 120
Symmetry Space Group P 61 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 CCD ADSC QUANTUM 315r 2014-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.97645 ALS 5.0.2
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 2.28 50 100 0.116 0.119 0.028 8.2 21.4 50185
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.28 2.32 100 0.339 0.927 20.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2Z5U 2.28 44.409 49937 2413 99.436 0.2 0.1981 0.1984 0.2299 0.2284 50.805
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] 1.279 0.639 1.279 -4.149
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.168 r_dihedral_angle_4_deg 17.992 r_dihedral_angle_3_deg 16.817 r_lrange_it 11.991 r_scangle_it 10.504 r_scbond_it 7.732 r_mcangle_it 7.418 r_dihedral_angle_1_deg 5.798 r_mcbond_it 5.701 r_angle_refined_deg 1.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.168 r_dihedral_angle_4_deg 17.992 r_dihedral_angle_3_deg 16.817 r_lrange_it 11.991 r_scangle_it 10.504 r_scbond_it 7.732 r_mcangle_it 7.418 r_dihedral_angle_1_deg 5.798 r_mcbond_it 5.701 r_angle_refined_deg 1.132 r_nbtor_refined 0.305 r_nbd_refined 0.198 r_symmetry_nbd_refined 0.15 r_symmetry_xyhbond_nbd_refined 0.146 r_xyhbond_nbd_refined 0.13 r_chiral_restr 0.085 r_gen_planes_refined 0.005 r_bond_refined_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5012 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 79
Software Software Software Name Purpose SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction