☰ Navigation Tabs
Crystal structure of the disulfide engineered HLA-A0201 molecule in complex with one GM dipeptide in the A pocket and one GM dipeptide in the F 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 2.34 47.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.643 α = 90 b = 84.124 β = 90 c = 83.716 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 1.6 84 96.9 0.069 1 9.7 3.4 103544
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 1.6 1.641 0.62 0.49
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 1.6 83.72 98243 5274 96.66 0.1713 0.169 0.1832 0.2139 0.2214 RANDOM 24.315
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] -10.92 -1.2 22.02 -11.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.87 r_dihedral_angle_4_deg 16.244 r_dihedral_angle_3_deg 14.599 r_dihedral_angle_1_deg 6.926 r_angle_refined_deg 1.658 r_angle_other_deg 1.022 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.87 r_dihedral_angle_4_deg 16.244 r_dihedral_angle_3_deg 14.599 r_dihedral_angle_1_deg 6.926 r_angle_refined_deg 1.658 r_angle_other_deg 1.022 r_chiral_restr 0.094 r_bond_refined_d 0.013 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 6212 Nucleic Acid Atoms Solvent Atoms 1173 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing