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MHC Class I A02 Allele presenting EAAGIGILTV, in complex with Mel8 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 293
Crystal Properties Matthews coefficient Solvent content 2.91 57.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.972 α = 90 b = 53.645 β = 94.333 c = 203.507 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 100 PIXEL DECTRIS EIGER2 X 16M 2019-01-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
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 3.24 99.7 100 0.28 0.328 0.22 0.995 2.7 3.7 34992 36.7
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 3.24 3.32 99.9 0.949 1.102 0.719 0.686 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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3HG1 3.24 99.686 34983 1742 99.894 0.229 0.2264 0.2272 0.2765 0.2731 56.356
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] -0.525 -0.611 -1.764 2.355
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.518 r_dihedral_angle_3_deg 19.074 r_dihedral_angle_4_deg 16.531 r_dihedral_angle_1_deg 8.226 r_angle_refined_deg 1.452 r_lrange_it 1.266 r_lrange_other 1.266 r_angle_other_deg 1.126 r_symmetry_xyhbond_nbd_refined 0.269 r_symmetry_nbd_refined 0.246
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.518 r_dihedral_angle_3_deg 19.074 r_dihedral_angle_4_deg 16.531 r_dihedral_angle_1_deg 8.226 r_angle_refined_deg 1.452 r_lrange_it 1.266 r_lrange_other 1.266 r_angle_other_deg 1.126 r_symmetry_xyhbond_nbd_refined 0.269 r_symmetry_nbd_refined 0.246 r_nbd_other 0.243 r_nbd_refined 0.21 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.169 r_ncsr_local_group_3 0.166 r_xyhbond_nbd_refined 0.16 r_ncsr_local_group_4 0.147 r_ncsr_local_group_2 0.111 r_ncsr_local_group_1 0.104 r_mcangle_it 0.081 r_mcangle_other 0.081 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.054 r_mcbond_it 0.043 r_mcbond_other 0.043 r_scangle_it 0.042 r_scangle_other 0.042 r_symmetry_xyhbond_nbd_other 0.034 r_scbond_it 0.022 r_scbond_other 0.022 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13160 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing