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DNA-encoded library (DEL)-enabled discovery of proximity inducing small molecules
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4W91 4W91
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 300 0.2 M NA2MALON, 20 %W/V PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.35 63.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.485 α = 90 b = 164.048 β = 90 c = 256.202 γ = 90
Symmetry Space Group P 21 21 21
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 2M 2020-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.97903 ALS 5.0.2
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 3.4 49.01 100 0.772 0.788 0.155 0.992 5.3 25 64886 76.05
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 3.4 3.48 100 3.442 1.3 0.71 0.343 24.4
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 4W91 3.4 49.01 1.34 64609 3221 99.69 0.2826 0.2804 0.2797 0.3242 0.3222 90.64
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 10.5367 f_angle_d 1.5413 f_chiral_restr 0.0889 f_plane_restr 0.0107 f_bond_d 0.0077
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21721 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 402
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction pointless data scaling AMoRE phasing