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Crystal structure of a truncated LSD1:CoREST in the presence of an LSD1-NT peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XBF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 The LSD1-CoREST complex 10mg/ml concentration (in 25 mM HEPES-Na, pH 7.4, 100 mM NaCl, 1 mM TCEP) was mixed (1:1) with the reservoir solution [0.60 M Li2SO4, 0.63 M (NH4)2SO4, 0.25 M NaCl, 100 mM Na-citrate, pH 5.6, 5 mM TCEP]. When get crystals, soak the crystals within 5mM LSD1-NT peptide.
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.783 α = 90 b = 179.164 β = 90 c = 234.907 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 CCD MARMOSAIC 225 mm CCD 2019-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.1 142.46 99.9 0.998 13.7 15 46959 83.45
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.21 0.764 1.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4XBF 3.1 100.72 1.34 46920 2290 99.91 0.2171 0.2161 0.2103 0.2358 0.2304 101.89
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 3.2559 f_angle_d 0.5785 f_chiral_restr 0.0407 f_plane_restr 0.0037 f_bond_d 0.0028
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6417 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement PHENIX refinement xia2 data reduction DIALS data scaling PHASER model building