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Crystal structure of Lsd18 in complex with a product
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 291.15 0.1 M Tris pH7.5, 1.0 M NaCl, 32% (w/v) PEG8000, 4% tert-butanol
Crystal Properties Matthews coefficient Solvent content 2.07 40.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.037 α = 74.79 b = 62.234 β = 81.97 c = 76.294 γ = 76.81
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 2021-01-31 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 2.2 19.612 98 0.126 0.136 0.052 0.995 10.7 6.9 40337
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 2.2 2.27 97.3 0.65 0.708 0.274 0.332 3.2 6.8
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 2.2 19.612 1.96 40284 1936 98.06 0.2291 0.227 0.2271 0.2712 0.271
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 20.711 f_angle_d 0.625 f_chiral_restr 0.044 f_plane_restr 0.005 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6971 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 159
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling MOLREP phasing