☰ Navigation Tabs
Crystal structure of the LSD1/CoREST histone demethylase in complex with the cofactor FAD and the inhibitor GSK690
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IW5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 100 mM ADA, 1.2 - 1.6M N/K and 3% w/v D-(+)-Glucose monohydrate
Crystal Properties Matthews coefficient Solvent content 7.27 83.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.487 α = 90 b = 179.407 β = 90 c = 235.058 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 105 CCD MARMOSAIC 300 mm CCD 2019-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.9762 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.66 37.46 99.1 0.2 0.2 0.996 7.9 13.8 141832
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.66 2.73 99.99 0.56 0.56 0.558
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.66 36.46 1.33 141830 3856 99.08 0.2397 0.2394 0.2421 0.2503 0.253
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.418 f_angle_d 1.691 f_chiral_restr 0.062 f_bond_d 0.014 f_plane_restr 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6253 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 28
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing