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How TCR-like antibody recognizes MHC-bound peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CVI PDB ENTRIES 3CVI AND 2VAA experimental model PDB 2VAA PDB ENTRIES 3CVI AND 2VAA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 293 0.2 M (NH4)2SO4, 0.1 M NaOAc, pH 4.6 containing 25% w/v polyethylene glycol 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.72 54.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.57 α = 90 b = 111.345 β = 90 c = 219.087 γ = 90
Symmetry Space Group P 21 21 21
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 2005-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A NSLS X4A
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 2.8 50 97.6 48272
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 2.8 2.9 95 0.429
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 ENTRIES 3CVI AND 2VAA 2.9 19.98 41343 2203 100 0.223 0.219 0.2215 0.296 0.2286 RANDOM 42.85
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] -0.4 -0.32 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.455 r_dihedral_angle_3_deg 18.148 r_dihedral_angle_4_deg 17.365 r_dihedral_angle_1_deg 5.569 r_scangle_it 1.326 r_angle_refined_deg 1.089 r_scbond_it 0.77 r_mcangle_it 0.617 r_mcbond_it 0.353 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.455 r_dihedral_angle_3_deg 18.148 r_dihedral_angle_4_deg 17.365 r_dihedral_angle_1_deg 5.569 r_scangle_it 1.326 r_angle_refined_deg 1.089 r_scbond_it 0.77 r_mcangle_it 0.617 r_mcbond_it 0.353 r_nbtor_refined 0.303 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.187 r_xyhbond_nbd_refined 0.149 r_symmetry_hbond_refined 0.147 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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_refined 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 12710 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction