☰ Navigation Tabs
PsiK from Psilocybe cubensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 100 mM HEPES pH 7.5, 2 M ammonium sulfate, 2% PEG 550 MME
Crystal Properties Matthews coefficient Solvent content 2.85 56.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.82 α = 90 b = 70.14 β = 95.837 c = 118.9 γ = 90
Symmetry Space Group C 1 2 1
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 X 2M KB mirror 2022-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8731 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.54 43.108 99.9 0.275 0.299 0.991 6.39 6.63 30400 60.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.54 2.61 99.9 2.641 2.859 0.35 0.91 6.85
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.54 43.108 30399 1483 99.859 0.2 0.1974 0.204 0.2433 0.2451 62.899
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] 1.121 1.009 -0.192 -1.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.071 r_dihedral_angle_6_deg 13.711 r_lrange_it 9.22 r_lrange_other 9.22 r_scangle_it 6.933 r_scangle_other 6.933 r_dihedral_angle_2_deg 6.913 r_dihedral_angle_1_deg 6.882 r_mcangle_it 5.536 r_mcangle_other 5.536
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.071 r_dihedral_angle_6_deg 13.711 r_lrange_it 9.22 r_lrange_other 9.22 r_scangle_it 6.933 r_scangle_other 6.933 r_dihedral_angle_2_deg 6.913 r_dihedral_angle_1_deg 6.882 r_mcangle_it 5.536 r_mcangle_other 5.536 r_scbond_it 4.355 r_scbond_other 4.354 r_mcbond_it 3.496 r_mcbond_other 3.493 r_angle_refined_deg 1.689 r_angle_other_deg 0.551 r_nbd_refined 0.219 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.151 r_nbd_other 0.133 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.074 r_ncsr_local_group_1 0.063 r_symmetry_nbd_refined 0.052 r_symmetry_xyhbond_nbd_refined 0.031 r_symmetry_xyhbond_nbd_other 0.015 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5684 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 101
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing