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Crystal structure of the LSD1/CoREST histone demethylase bound to its nucleosome substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LZ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.5 277 25 mM HEPES pH7.5,
75 mM triammonium citrate,
10% PEG2000-MME,
Modified Microbatch under oil
Crystal Properties Matthews coefficient Solvent content 3.98 69.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.771 α = 90 b = 335.77 β = 91.07 c = 174.633 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2017-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 4.99 20.17 98.2 0.079 0.093 0.05 0.998 8.1 3.5 50839
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 4.99 5.15 99.9 1.34 1.575 0.822 0.352 3.6
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 THROUGHOUT 3LZ0 4.99 20.17 1.34 50660 1978 99.33 0.2309 0.2291 0.231 0.2774 0.2827 415.2764
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 18.915 f_angle_d 0.468 f_chiral_restr 0.033 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 37122 Nucleic Acid Atoms 15662 Solvent Atoms Heterogen Atoms 212
Software Software Software Name Purpose PHENIX refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing