☰ Navigation Tabs
Crystal structure of LSD1 in complex with compound 5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6KGP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1M MES (pH 6.2-6.3), 0.2M diammonium tartrate, 0.0005M TCEP, 10-12% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.56 65.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 185.256 α = 90 b = 185.256 β = 90 c = 106.881 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 RAYONIX MX225-HS 2018-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.000 SPring-8 BL26B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim 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 2.91 47.83 99.9 0.121 0.125 0.029 0.999 20.5 18.4 24188 87.46
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.91 3.09 99.7 1.916 1.972 0.45 0.75 2.1 18.7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6KGP 2.91 47.83 0.31 24171 1263 99.79 0.2114 0.2087 0.2582 0.2285 97.72
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 15.682 f_angle_d 1.3364 f_chiral_restr 0.0692 f_plane_restr 0.0109 f_bond_d 0.0101
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5069 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 108
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing