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Crystal structure of the great reed warbler MHC class I in complex with an 8-mer peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ZQJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 28 % PEG4000, 0.1 M MgCl2 and 0.1 M Tris/HCl pH 8.5 with seeding
Crystal Properties Matthews coefficient Solvent content 2.12 41.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 205.947 α = 90 b = 49.038 β = 94.69 c = 39.38 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 PIXEL DECTRIS EIGER X 16M 2023-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.976254 MAX IV BioMAX
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 2.15 47.7 99.6 0.059 0.071 0.038 0.998 10.7 3.4 21449
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 2.15 2.22 99.9 0.733 0.872 0.468 0.753 3.4
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 THROUGHOUT 2.15 47.7 1.27 21416 1116 99.29 0.2089 0.2057 0.2056 0.2658 0.2657
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 20.141 f_angle_d 0.545 f_chiral_restr 0.044 f_plane_restr 0.005 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3095 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 36
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing