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Crystal structure of murine P14 TCR/ H-2Db complex with PA, modified gp33 peptide from LCMV
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S7U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 280 19% PEG 6000, 0.1M Tris HCl pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.75 55.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 255.926 α = 90 b = 46.542 β = 94.34 c = 89.398 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 PIXEL DECTRIS PILATUS 6M-F 2016-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.972 ESRF ID23-1
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 1.95 127.6 98.8 0.048 13.2 2.8 76281
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 1.95 1.99 96.1 0.603 1.8 2.8 4331
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 1s7u 1.95 127.6 72450 3830 98.61 0.19736 0.19569 0.2046 0.22868 0.2366 RANDOM 38.731
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] -0.19 0.03 0.17 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.819 r_dihedral_angle_4_deg 16.275 r_dihedral_angle_3_deg 15.659 r_dihedral_angle_1_deg 7.123 r_long_range_B_refined 6.037 r_long_range_B_other 5.936 r_scangle_other 2.172 r_mcangle_it 1.798 r_mcangle_other 1.798 r_angle_refined_deg 1.686
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.819 r_dihedral_angle_4_deg 16.275 r_dihedral_angle_3_deg 15.659 r_dihedral_angle_1_deg 7.123 r_long_range_B_refined 6.037 r_long_range_B_other 5.936 r_scangle_other 2.172 r_mcangle_it 1.798 r_mcangle_other 1.798 r_angle_refined_deg 1.686 r_scbond_it 1.359 r_scbond_other 1.344 r_mcbond_it 1.093 r_mcbond_other 1.092 r_angle_other_deg 0.978 r_chiral_restr 0.103 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6512 Nucleic Acid Atoms Solvent Atoms 353 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing