☰ Navigation Tabs
Crystal structure of the T-cell receptor NYE_S2 bound to HLA A2*01-SLLMWITQV
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5E00 5e00 (chains A and B), 3REV (chain A) and 4DZB (chain B) experimental model PDB 3REV 5e00 (chains A and B), 3REV (chain A) and 4DZB (chain B) experimental model PDB 4DZB 5e00 (chains A and B), 3REV (chain A) and 4DZB (chain B)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.02 M sodium/potassium phosphate, 20 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.26 62.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.16 α = 90 b = 84.25 β = 129.81 c = 111.51 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 PILATUS 6M-F 2017-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.56 66.51 99.3 0.064 0.025 0.999 17.9 7.66 37679
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.56 2.6 99.7 2.07 0.775 0.637 0.96 7.94
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 5e00 (chains A and B), 3REV (chain A) and 4DZB (chain B) 2.56 66.51 37679 1945 99.31 0.25209 0.2499 0.2517 0.29324 0.2965 RANDOM 80.735
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] 3.15 -3.46 3.12 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.197 r_dihedral_angle_3_deg 14.575 r_dihedral_angle_4_deg 13.361 r_long_range_B_refined 9.727 r_long_range_B_other 9.727 r_dihedral_angle_1_deg 6.076 r_mcangle_it 5.427 r_mcangle_other 5.427 r_scangle_other 4.541 r_mcbond_it 3.256
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.197 r_dihedral_angle_3_deg 14.575 r_dihedral_angle_4_deg 13.361 r_long_range_B_refined 9.727 r_long_range_B_other 9.727 r_dihedral_angle_1_deg 6.076 r_mcangle_it 5.427 r_mcangle_other 5.427 r_scangle_other 4.541 r_mcbond_it 3.256 r_mcbond_other 3.253 r_scbond_it 2.606 r_scbond_other 2.605 r_angle_refined_deg 1.155 r_angle_other_deg 0.846 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6277 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing