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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 4E41 PDB entry 4E41
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5 298 1.5 M sodium nitrate
0.1 M sodium citrate, pH 5.0, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.47 64.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.07 α = 90 b = 75.365 β = 123.48 c = 130.859 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 2010-09-26 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) R Merge 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 2.7 50 99 0.081 25.8 6.9 37490 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 2.7 2.8 99 0.122 17.8 6.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 4E41 2.7 44.63 35795 1908 99.91 0.20347 0.20033 0.1986 0.26263 0.2578 RANDOM 41.376
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] -1.3 -1.35 0.55 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.01 r_dihedral_angle_3_deg 18.274 r_dihedral_angle_4_deg 18.265 r_dihedral_angle_1_deg 9.878 r_scangle_it 2.546 r_scbond_it 1.468 r_angle_refined_deg 1.437 r_mcangle_it 1.235 r_mcbond_it 0.643 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.01 r_dihedral_angle_3_deg 18.274 r_dihedral_angle_4_deg 18.265 r_dihedral_angle_1_deg 9.878 r_scangle_it 2.546 r_scbond_it 1.468 r_angle_refined_deg 1.437 r_mcangle_it 1.235 r_mcbond_it 0.643 r_nbtor_refined 0.308 r_metal_ion_refined 0.236 r_nbd_refined 0.222 r_symmetry_vdw_refined 0.197 r_xyhbond_nbd_refined 0.158 r_symmetry_hbond_refined 0.131 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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 6621 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 19
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling