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PsiM in complex with sinefungin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8PB8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 20% PEG 8000, 200 mM MgCl2, 2.1 mM psilocybin, 100 mM Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.29 46.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.963 α = 90 b = 78.37 β = 90 c = 83.818 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 EIGER2 X CdTe 16M 2023-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.6888 ESRF ID23-1
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 1.04 32.11 99.98 0.05481 0.05712 0.01592 0.999 18.22 13.1 305456 12.57
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.04 1.077 1.249 0.3627 0.78 1.71
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 1.04 32.11 1.12 305456 15565 99.98 0.1464 0.1455 0.1455 0.1641 0.1652 20
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 7.1811 f_angle_d 1.2045 f_chiral_restr 0.0968 f_plane_restr 0.0136 f_bond_d 0.0108
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2494 Nucleic Acid Atoms Solvent Atoms 449 Heterogen Atoms 29
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing