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The structure of the MHC class I molecule of bony fishes provides insights into the conserved nature of the antigen-presenting system
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YEZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.2 M ammonium citrate tribasic, pH 7.0 and 20% w/v polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.34 47.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.28 α = 90 b = 50.413 β = 124.08 c = 86.077 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 CCD ADSC QUANTUM 315 2010-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97931 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.9 50 99 17.711 3.2 31840
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 NONE 2YEZ 1.901 32.883 0.1 31840 1622 94.7 0.1918 0.1902 0.193 0.2235 0.2248
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] -1.142 -0.6788 4.0645 -2.9225
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.966 f_angle_d 0.765 f_chiral_restr 0.059 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3053 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing