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Crystal structure of shark nonclassical MHC CLASS I, UGA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Morpheus H8:
37.5 % v/v Precipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350),
0.1 M Sodium HEPES; MOPS
(acid) pH 7.5,
0.1 M Amino acids
Crystal Properties Matthews coefficient Solvent content 2.92 57.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 165.773 α = 90 b = 95.628 β = 123.96 c = 112.372 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 80 PIXEL DECTRIS EIGER X 16M 2022-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979180 APS 24-ID-E
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 2.67 93.2 99.6 0.291 0.314 0.119 0.987 6.5 7 41251
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.67 2.78 99 1.55 1.674 0.627 0.522 7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.67 93.2 1.35 41199 1979 99.43 0.2405 0.2394 0.2437 0.2617 0.2663
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 20.537 f_angle_d 1.625 f_chiral_restr 0.101 f_plane_restr 0.023 f_bond_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8956 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 290
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing