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Computational Stabilization of T Cell Receptor Constant Domains
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F53
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 23% PEG 4K, 300 mM magnesium sulfate, 10% glycerol
Crystal Properties Matthews coefficient Solvent content 3.09 60.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.854 α = 90 b = 59.852 β = 110.24 c = 61.352 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 6M Kohzu HLD-4 with diamond 111 crystals 2018-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
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 1.76 29.33 99.2 0.067 0.078 0.04 0.999 5.6 3.8 32373
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 1.76 1.86 99.1 1.114 1.296 0.658 0.588 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2F53 1.76 29.33 30717 1642 99.14 0.2027 0.2015 0.2261 0.245 RANDOM 30.088
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] 0.75 -0.86 1.26 -1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.353 r_dihedral_angle_3_deg 12.184 r_dihedral_angle_4_deg 7.85 r_dihedral_angle_1_deg 5.878 r_angle_refined_deg 1.24 r_angle_other_deg 0.736 r_chiral_restr 0.074 r_bond_refined_d 0.007 r_bond_other_d 0.006 r_gen_planes_refined 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.353 r_dihedral_angle_3_deg 12.184 r_dihedral_angle_4_deg 7.85 r_dihedral_angle_1_deg 5.878 r_angle_refined_deg 1.24 r_angle_other_deg 0.736 r_chiral_restr 0.074 r_bond_refined_d 0.007 r_bond_other_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1718 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 3
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction