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Crystal structure of the ternary complex between human T cell receptor, staphylococcal enterotoxin H and human major histocompatibility complex class II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OGA PDB ENTRY 1OGA CHAINS D, E AND PDB ENTRY 1HXY CHAINS A, B, D experimental model PDB 1HXY PDB ENTRY 1OGA CHAINS D, E AND PDB ENTRY 1HXY CHAINS A, B, D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 15% W/V PEG 5000 MME, 0.1 M BIS-TRIS PH 7.0, 0.1 M NACL
Crystal Properties Matthews coefficient Solvent content 2.9 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 191.18 α = 90 b = 48.89 β = 113.55 c = 166.72 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 CCD TOROIDAL MIRRORS 2009-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2.3 42.72 97.6 0.08 10.3 3.2 61858 2 49.17
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 2.3 2.42 88.8 0.45 2.1 2.7
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 1OGA CHAINS D, E AND PDB ENTRY 1HXY CHAINS A, B, D 2.3 152.5 58700 3148 97.17 0.22414 0.2215 0.2168 0.27236 0.2657 RANDOM 38.997
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] -2.75 -1.62 2.02 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.53 r_dihedral_angle_4_deg 19.71 r_dihedral_angle_3_deg 18.278 r_dihedral_angle_1_deg 6.671 r_scangle_it 3.061 r_scbond_it 1.875 r_mcangle_it 1.488 r_angle_refined_deg 1.443 r_mcbond_it 0.794 r_chiral_restr 0.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.53 r_dihedral_angle_4_deg 19.71 r_dihedral_angle_3_deg 18.278 r_dihedral_angle_1_deg 6.671 r_scangle_it 3.061 r_scbond_it 1.875 r_mcangle_it 1.488 r_angle_refined_deg 1.443 r_mcbond_it 0.794 r_chiral_restr 0.096 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8266 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing