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Crystal structure of the disulfide engineered HLA-A0201 molecule in complex with one GL dipeptide in the A pocket.
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 2.57 52.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.34 α = 90 b = 81.134 β = 112.29 c = 56.45 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 1.4 81 100 0.03 1 14.2 3.4 86442
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 1.4 1.436 0.54 0.64
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 1.4 52.23 82046 4366 98.9 0.1919 0.1901 0.1945 0.2267 0.2306 RANDOM 21.744
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] 1.13 -0.9 -0.78 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.402 r_dihedral_angle_4_deg 17.739 r_dihedral_angle_3_deg 13.057 r_dihedral_angle_1_deg 6.656 r_angle_refined_deg 1.763 r_angle_other_deg 1.069 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.402 r_dihedral_angle_4_deg 17.739 r_dihedral_angle_3_deg 13.057 r_dihedral_angle_1_deg 6.656 r_angle_refined_deg 1.763 r_angle_other_deg 1.069 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3077 Nucleic Acid Atoms Solvent Atoms 471 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing