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Crystal Structure of HLA A*2402 in complex with TYQWIIRNWET, an 11-mer epitope from Influenza
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4F7M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 277 24% PEG8000, 0.1 HEPES pH 7.5, 5% v/v Ethyl acetate
Crystal Properties Matthews coefficient Solvent content 2.54 51.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.678 α = 90 b = 43.645 β = 95.56 c = 236.491 γ = 90
Symmetry Space Group I 1 2 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 EIGER X 16M 2018-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.98 Australian Synchrotron MX2
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 2.95 39.23 99.6 0.091 0.995 12.3 3.7 19624 78.39
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.95 3.13 0.404
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 4F7M 2.95 39.21 19617 989 99.4 0.212 0.208 0.2175 0.275 0.287 RANDOM 64.69
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] 10.6467 -4.1792 -6.6209 -4.0259
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 22.47 t_omega_torsion 2.7 t_angle_deg 1.11 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 22.47 t_omega_torsion 2.7 t_angle_deg 1.11 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6291 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction