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Crystal structure of the disulfide engineered HLA-A0201 molecule devoid of peptide (annealed)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Q3K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.1 M HEPES pH 7.5,
20% PEG 10 000, 8% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.33 47.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.728 α = 90 b = 82.735 β = 90.06 c = 83.891 γ = 90
Symmetry Space Group P 1 21 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 PILATUS3 6M 2018-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.987 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.75 84 94.2 0.095 1 7.3 2.7 76159
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.794 0.72 0.57
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6Q3K 1.75 83.89 72515 3641 93.86 0.179 0.1765 0.1826 0.2299 0.236 RANDOM 22.339
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] -11.73 5.85 26.09 -14.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.937 r_dihedral_angle_4_deg 19.022 r_dihedral_angle_3_deg 14.24 r_dihedral_angle_1_deg 7.197 r_angle_refined_deg 1.563 r_angle_other_deg 0.922 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.937 r_dihedral_angle_4_deg 19.022 r_dihedral_angle_3_deg 14.24 r_dihedral_angle_1_deg 7.197 r_angle_refined_deg 1.563 r_angle_other_deg 0.922 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6161 Nucleic Acid Atoms Solvent Atoms 1142 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing