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Improved High Resolution Structure of MHC Class II complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4X5W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.2 M Na Acetate
0.1 M TRIS
30 %w/v PEG 4K
Crystal Properties Matthews coefficient Solvent content 2.47 50.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.153 α = 90 b = 60.002 β = 108.75 c = 51.713 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 PILATUS 6M-F 2018-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.978 Diamond I04-1
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 1.7 26.85 99.75 0.052 0.057 0.023 1 18.4 6 294236 21.85
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 1.7 1.76 99.6 0.71 0.78 0.31 0.88 2.3 6
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 4x5w 1.7 26.85 1.34 49389 4990 99.53 0.1747 0.1715 0.1714 0.2021 0.2016 35.61
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 6.6887 f_angle_d 1.1217 f_chiral_restr 0.0759 f_bond_d 0.0127 f_plane_restr 0.0085
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3027 Nucleic Acid Atoms Solvent Atoms 317 Heterogen Atoms 22
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction SCALA data scaling PHENIX phasing