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Crystal structure of de novo designed serotonin binder SROb2_26_L7F
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 BATCH MODE 291 25.5% (w/v) PEG 4000, 170 mM Ammonium sulfate, 15% (v/v) Glycerol
Crystal Properties Matthews coefficient Solvent content 2.05 40.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.501 α = 90 b = 65.893 β = 90.7 c = 29.513 γ = 90
Symmetry Space Group P 1 21 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 2024-05-25 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 26.93 98.96 0.996 16.88 3.1 7301 17.91
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 2.13 0.1238 0.1481 0.0798 0.969 6.83
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 26.93 0.06 7301 774 98.96 0.2021 0.2016 0.2341 0.2338
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 16.942 f_angle_d 0.887 f_chiral_restr 0.045 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 938 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 25
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