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CRYSTAL STRUCTURES OF MURINE MHC CLASS I H-2 Db AND Kb MOLECULES IN COMPLEX WITH CTL EPITOPES FROM INFLUENZA A VIRUS: IMPLICATIONS FOR TCR REPERTOIRE SELECTION AND IMMUNODOMINANCE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JPF PDB ENTRY 1JPF
Crystallization Crystal Properties Matthews coefficient Solvent content 2.47 50.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.552 α = 90 b = 56.552 β = 90 c = 277.654 γ = 90
Symmetry Space Group P 43 21 2
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 CUSTOM M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
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 50 99.4 0.09 21.5 6 19939
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 2.36 100 0.65 2.7 5.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1JPF 2.3 29.58 19938 1072 99.5 0.234 0.23 0.304 0.2736 RANDOM 32.98
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] 0.05 0.05 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.866 r_dihedral_angle_4_deg 20.718 r_dihedral_angle_3_deg 18.617 r_dihedral_angle_1_deg 6.187 r_scangle_it 2.386 r_scbond_it 1.462 r_angle_refined_deg 1.219 r_mcangle_it 1.155 r_mcbond_it 0.648 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.866 r_dihedral_angle_4_deg 20.718 r_dihedral_angle_3_deg 18.617 r_dihedral_angle_1_deg 6.187 r_scangle_it 2.386 r_scbond_it 1.462 r_angle_refined_deg 1.219 r_mcangle_it 1.155 r_mcbond_it 0.648 r_nbtor_refined 0.299 r_symmetry_hbond_refined 0.221 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.179 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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_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 3164 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling AMoRE phasing