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Crystal structure of Lsd18 in complex with ligands
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8UP4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 0.1 M Tris pH7.5, 1.0 M NaCl, 32% (w/v) PEG8000, 4% tert-butanol
Crystal Properties Matthews coefficient Solvent content 2.03 39.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.921 α = 74.61 b = 61.804 β = 81.74 c = 75.633 γ = 76.79
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 PILATUS 6M 2020-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97915 SSRF BL18U1
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 1.75 25.284 95.26 0.145 0.206 0.145 0.885 8.5 1 76354
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 1.75 1.813 86.63 0.437 0.293 0.528 0.8 4.1
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 8UP4 1.75 25.284 1.99 76322 3773 95.29 0.2105 0.2085 0.2085 0.2488 0.2487
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 20.176 f_angle_d 0.855 f_chiral_restr 0.054 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6899 Nucleic Acid Atoms Solvent Atoms 806 Heterogen Atoms 153
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction Aimless data scaling MOLREP phasing