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Structure of the MHC class Ib molecule Qa-1b in complex with Q001 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VJ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 8% PEG4000, 0.1M sodium acetate (pH 5.7) and 10 mM NiCl2
Crystal Properties Matthews coefficient Solvent content 2.41 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.56 α = 90 b = 72.797 β = 90 c = 96.515 γ = 90
Symmetry Space Group P 21 21 21
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 2022-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.97625 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 2.43 50.69 99.93 0.0337 0.04766 0.0337 0.999 13.23 2 16416 42.52
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 2.43 2.517 99.88 0.2549 0.3604 0.2549 0.895 2
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 2.43 50.69 1.35 16416 823 99.94 0.1939 0.1912 0.1942 0.247 0.2551 47.38
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 6.8431 f_angle_d 0.9858 f_chiral_restr 0.0554 f_plane_restr 0.0091 f_bond_d 0.0079
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3182 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement PHENIX refinement AutoProcess data reduction TRUNCATE data scaling PHENIX phasing