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Structural basis for the recognition of mutant self by a tumor-specific, MHC class II-restricted T cell receptor G4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IAM PDB entry 2IAM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 298 20% (wt/vol) polyethylene glycol 1000, 0.2 M calcium acetate, 0.1 M imidazole, pH 8.0, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.43 49.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.133 α = 90 b = 175.611 β = 110.75 c = 88.646 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 CCD ADSC QUANTUM 315 2007-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 30 97.2 53716 2 2
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 2.6 2.7 83.8 0.269 2.6 3.1
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 PDB entry 2IAM 2.6 30 51068 2704 97.23 0.20076 0.19743 0.26374 0.248 RANDOM 49.044
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] -1.52 -1.31 -0.69 1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.804 r_dihedral_angle_3_deg 19.04 r_dihedral_angle_4_deg 18.972 r_dihedral_angle_1_deg 10.922 r_scangle_it 2.537 r_angle_refined_deg 1.687 r_scbond_it 1.491 r_mcangle_it 1.227 r_mcbond_it 0.641 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.804 r_dihedral_angle_3_deg 19.04 r_dihedral_angle_4_deg 18.972 r_dihedral_angle_1_deg 10.922 r_scangle_it 2.537 r_angle_refined_deg 1.687 r_scbond_it 1.491 r_mcangle_it 1.227 r_mcbond_it 0.641 r_nbtor_refined 0.31 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.215 r_symmetry_hbond_refined 0.182 r_xyhbond_nbd_refined 0.153 r_metal_ion_refined 0.099 r_chiral_restr 0.094 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12805 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 2
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling