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Structure of a MHC I-Tapasin-ERp57 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ENY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 100 mM Gly-Gly, AMPD, pH 8.5, 300 mM lithium sulfate, 300 mM sodium sulfate, 300 mM potassium sulfate, 20% (v/v) PEG8000, 40% (v/v) 1,5-pentanediol
Crystal Properties Matthews coefficient Solvent content 4.04 69.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.76 α = 90 b = 168.53 β = 90 c = 187.05 γ = 90
Symmetry Space Group P 2 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 PILATUS 6M 2020-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.033 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.7 48 99.76 0.998 14.9 5.9 65719 87.61
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.797 0.443
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 6ENY 2.7 48 1.34 65719 3284 99.76 0.1999 0.1983 0.2064 0.2289 0.2313 106.17
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 12.3171 f_angle_d 1.3565 f_chiral_restr 0.0815 f_bond_d 0.0094 f_plane_restr 0.0049
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9621 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 48
Software Software Software Name Purpose PDB-REDO refinement PHENIX refinement XDS data reduction XDS data scaling PHASER phasing