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Structure of a designed minibinder to NYESO1-A*02:01
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7SR0 in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 0.2 M ammonium acetate
0.1 M bis-tris pH 5.5
25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.5 50.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.452 α = 90 b = 98.536 β = 90 c = 155.743 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 S 9M 2024-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1 ALS 8.2.1
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 2.05 49.27 99.17 0.3252 0.3326 0.0686 0.999 8.49 23.3 92563 33.16
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 2.05 2.12 100 3.471 3.545 0.7168 0.349 1.45 24
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 2.05 49.27 1.33 91895 1384 99.17 0.255 0.2548 0.2549 0.2673 0.2672 60.86
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 13.915 f_angle_d 0.5214 f_chiral_restr 0.0384 f_plane_restr 0.005 f_bond_d 0.0025
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10112 Nucleic Acid Atoms Solvent Atoms 270 Heterogen Atoms 96
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing