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MHC Class I A02 Allele presenting LLLGIGILVL, in complex with Mel5 TCR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HG1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1M TRIS, 15% PEG 8000, 15% Glycerol, pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.26 62.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.019 α = 90 b = 122.019 β = 90 c = 82.418 γ = 90
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 X 16M 2020-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97951 Diamond I04
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 2.1 61.02 100 0.105 0.113 0.04 0.998 10.6 7.7 70731 44
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 2.1 2.14 100 2.6 2.8 0.989 0.312 7.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3HG1 2.1 61.01 67098 3454 99.78 0.2064 0.2045 0.2114 0.2432 0.2448 RANDOM 63.387
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 -1 1.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.952 r_dihedral_angle_4_deg 19.777 r_dihedral_angle_3_deg 17.391 r_dihedral_angle_1_deg 8.602 r_angle_refined_deg 1.676 r_angle_other_deg 1.264 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.952 r_dihedral_angle_4_deg 19.777 r_dihedral_angle_3_deg 17.391 r_dihedral_angle_1_deg 8.602 r_angle_refined_deg 1.676 r_angle_other_deg 1.264 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6629 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 24
Software Software Software Name Purpose XDS data reduction xia2 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction