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Xenoreactive complex AHIII 12.2 TCR bound to p1049/HLA-A2.1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B0G Class I MHC, PDB ENTRY 1B0G. TCR, PDB ENTRY 2CKB experimental model PDB 2CKB Class I MHC, PDB ENTRY 1B0G. TCR, PDB ENTRY 2CKB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 PEG3350, 25mM MES , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.57 52.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.708 α = 90 b = 84.469 β = 92.13 c = 121.336 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 CCD ADSC QUANTUM 4 Bent Cylinder, 1:1 defocused rhodium-coated electroless nickel-plated bent aluminum cylinder 2001-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12B 1.01715 NSLS X12B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 30 99.9 0.074 28.5 7.5 122580 121366
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 99.9 0.578 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 Class I MHC, PDB ENTRY 1B0G.
TCR, PDB ENTRY 2CKB 2 30 122580 121366 6421 99.99 0.23 0.22058 0.21887 0.2298 0.25293 0.2609 RANDOM 14.229
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] 1.18 0.98 0.59 -1.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.406 r_dihedral_angle_1_deg 4.288 r_sphericity_free 3.612 r_scangle_it 2.228 r_scbond_it 1.507 r_angle_refined_deg 1.435 r_sphericity_bonded 1.083 r_mcangle_it 1.067 r_rigid_bond_restr 0.902 r_angle_other_deg 0.811
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.406 r_dihedral_angle_1_deg 4.288 r_sphericity_free 3.612 r_scangle_it 2.228 r_scbond_it 1.507 r_angle_refined_deg 1.435 r_sphericity_bonded 1.083 r_mcangle_it 1.067 r_rigid_bond_restr 0.902 r_angle_other_deg 0.811 r_mcbond_it 0.658 r_symmetry_hbond_other 0.532 r_symmetry_hbond_refined 0.371 r_xyhbond_nbd_other 0.357 r_symmetry_vdw_refined 0.334 r_symmetry_vdw_other 0.328 r_nbd_refined 0.284 r_nbd_other 0.229 r_xyhbond_nbd_refined 0.188 r_chiral_restr 0.09 r_nbtor_other 0.065 r_gen_planes_other 0.049 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13136 Nucleic Acid Atoms Solvent Atoms 416 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling AMoRE phasing REFMAC refinement HKL-2000 data reduction