☰ Navigation Tabs
Crystal structure of de novo designed serotonin binder SROb2_30
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other de novo designed model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7.5 291 20% (w/v) PEG 10,000;100 mM HEPES Sodium hydroxide; pH 7.5
Crystal Properties Matthews coefficient Solvent content 1.87 34.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.33 α = 90 b = 42.76 β = 100.71 c = 86.305 γ = 90
Symmetry Space Group I 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 181 PIXEL RIGAKU HyPix-6000HE 2024-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE Cu FINE FOCUS 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 27.24 81.06 0.999 6.99 4 13551
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.09 0.126
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 2.58 27.24 0.03 5806 591 90.89 0.3058 0.298 0.3132 0.3673 0.3464
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 21.703 f_angle_d 0.996 f_chiral_restr 0.042 f_bond_d 0.008 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1398 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 56
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction PHENIX model building Coot model building PHASER phasing CrysalisPro data reduction CrysalisPro data scaling