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Crystal Structure of HLA-A68 presenting a C-terminally extended peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HWZ Ensemble of 4HWZ, 5T6X, 4RMU, 4HWZ experimental model PDB 5T6X Ensemble of 4HWZ, 5T6X, 4RMU, 4HWZ experimental model PDB 4RMU Ensemble of 4HWZ, 5T6X, 4RMU, 4HWZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 12% PEG3350
0.005M cobalt chloride
0.005M cadmium chloride
0.005M nickel chloride
0.005M magnesium chloride
0.1M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.93 58.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.061 α = 90 b = 80.247 β = 90 c = 110.88 γ = 90
Symmetry Space Group P 21 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 PILATUS3 6M 2017-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96864 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.61 29.531 99.9 0.094 0.103 0.04 11.3 6.6 68846 68846
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.61 1.7 99.5 0.602 0.602 0.654 0.253 1.3 6.6
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 Ensemble of 4HWZ, 5T6X, 4RMU, 4HWZ 1.61 29.53 66856 1917 99.81 0.1586 0.1579 0.1701 0.1814 0.191 RANDOM 20.343
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] -0.21 0.09 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.837 r_dihedral_angle_4_deg 18.963 r_dihedral_angle_3_deg 11.428 r_dihedral_angle_1_deg 6.619 r_angle_refined_deg 1.714 r_angle_other_deg 1.035 r_chiral_restr 0.116 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.837 r_dihedral_angle_4_deg 18.963 r_dihedral_angle_3_deg 11.428 r_dihedral_angle_1_deg 6.619 r_angle_refined_deg 1.714 r_angle_other_deg 1.035 r_chiral_restr 0.116 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3131 Nucleic Acid Atoms Solvent Atoms 442 Heterogen Atoms 29
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction SCALA data reduction