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Structure of F11TCR in complex with DR1 MHC Class II presenting PKYVKQNTLKLAT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FYT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 291 0.1 M Na Cacodylate,
0.2 M NH4 SO4, 15 %
PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.24 62.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.28 α = 90 b = 184.9 β = 90 c = 50.2 γ = 90
Symmetry Space Group P 21 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 PIXEL DECTRIS PILATUS3 S 6M 2015-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97623 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.91 92.46 99.9 0.078 0.084 0.031 0.999 14.1 7.2 96543 39.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.91 1.96 99.9 1.26 1.354 0.491 7.4
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1FYT 1.91 92.45 96461 4763 99.905 0.207 0.2055 0.2122 0.2332 0.2431 49.547
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] -0.331 -0.679 1.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.264 r_dihedral_angle_1_deg 18.656 r_dihedral_angle_4_deg 17.013 r_dihedral_angle_3_deg 15.772 r_dihedral_angle_other_3_deg 11.667 r_lrange_other 6.543 r_lrange_it 6.542 r_scangle_it 3.382 r_scangle_other 3.382 r_mcangle_it 2.556
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.264 r_dihedral_angle_1_deg 18.656 r_dihedral_angle_4_deg 17.013 r_dihedral_angle_3_deg 15.772 r_dihedral_angle_other_3_deg 11.667 r_lrange_other 6.543 r_lrange_it 6.542 r_scangle_it 3.382 r_scangle_other 3.382 r_mcangle_it 2.556 r_mcangle_other 2.555 r_scbond_it 2.219 r_scbond_other 2.219 r_angle_refined_deg 1.709 r_mcbond_it 1.613 r_mcbond_other 1.613 r_angle_other_deg 1.316 r_symmetry_nbd_refined 0.265 r_nbd_other 0.215 r_nbd_refined 0.201 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.168 r_symmetry_xyhbond_nbd_refined 0.167 r_xyhbond_nbd_refined 0.142 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6567 Nucleic Acid Atoms Solvent Atoms 308 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling XDS data scaling PHASER phasing