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LSD1-CoREST in complex with GSK-LSD1 and peptide PRCALVKSK
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V1D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 1.2 Na/K Tartrate, 100 mM ADA pH 6.5
Crystal Properties Matthews coefficient Solvent content 5.63 78.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.294 α = 90 b = 181.646 β = 90 c = 233.847 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 PIXEL DECTRIS PILATUS3 6M 2024-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96546 ESRF MASSIF-1
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 2.67 49.16 98.3 0.06 0.069 0.033 0.998 12.1 3.9 68980
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 2.78 2.88 99.4 0.849 0.988 0.491 0.56 3.9
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 2.78 49.16 1.34 62635 2000 97.95 0.216 0.2151 0.2448 0.2417 0.2612
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 10.219 f_angle_d 1.56 f_chiral_restr 0.073 f_bond_d 0.01 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6346 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 63
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction PHASER phasing XDS data reduction