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Crystal Structure of HLA B*3503 in complex with NPDIVIYQY, an 9-mer epitope from HIV-I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LNR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.1M HEPES, 20% PEG8000
Crystal Properties Matthews coefficient Solvent content 2.56 51.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.898 α = 90 b = 81.706 β = 90 c = 110.024 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 EIGER X 16M 2020-11-30 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) Rrim I (All) Rpim I (All) 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 1.9 46.19 99.9 0.139 0.156 0.07 0.992 7.5 4.9 36900 23.91
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 100 0.952 1.073 0.485 0.696 4.9
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 4lnr 1.9 46.19 36845 1900 99.8 0.2039 0.2023 0.2061 0.2321 0.2376 RANDOM 25.03
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] 3.3435 4.6046 -7.9481
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.07 t_omega_torsion 3.71 t_angle_deg 0.92 t_bond_d 0.008 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 16.07 t_omega_torsion 3.71 t_angle_deg 0.92 t_bond_d 0.008 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 3159 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 6
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing BUSTER refinement PDB_EXTRACT data extraction