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Crystal structure of Fab.34.5.8 in complex with MHC-I (H2-Dd)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WEU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 18% PEG4000, 0.1 M MES, pH 6.0, 0.12 M calcium acetate
Crystal Properties Matthews coefficient Solvent content 2.71 54.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.087 α = 90 b = 50.892 β = 90 c = 224.825 γ = 90
Symmetry Space Group P 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 273 PIXEL DECTRIS EIGER X 16M 2022-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.69 87.09 97.9 0.145 0.085 0.99 7.6 3.8 54120 57.76
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.69 2.8 99.3 0.927 0.455 0.565 1.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 5WEU 2.69 87.09 154.07 54120 2738 97.43 0.2085 0.2009 0.2114 0.2425 0.2406 60.4
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.429 f_angle_d 0.7559 f_chiral_restr 0.0479 f_plane_restr 0.006 f_bond_d 0.0045
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12393 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 42
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing