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HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential HIV-1 escape through identical epitopes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4I4W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 291 0.1 M TRIS pH 8.0, 15% PEG 4000 and 15% glycerol
Crystal Properties Matthews coefficient Solvent content 2.68 54.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.02 α = 91.13 b = 49.06 β = 93.53 c = 107.84 γ = 95.7
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 PSI PILATUS 6M mirrors 2012-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.06 53.8 97.7 0.102 0.092 0.986 5.8 2 56594
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.06 2.11 96.9 0.407 0.367 0.811 2.3 2 4139
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 4I4W 2.06 53.8 56593 2874 97.74 0.1746 0.1727 0.1809 0.2087 0.214 RANDOM 48.678
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] -0.65 0.06 -0.52 -1.47 -0.37 2.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.423 r_dihedral_angle_4_deg 19.223 r_dihedral_angle_3_deg 18.116 r_dihedral_angle_1_deg 7.132 r_mcangle_it 4.314 r_mcbond_it 2.855 r_mcbond_other 2.855 r_angle_refined_deg 1.848 r_angle_other_deg 1.185 r_chiral_restr 0.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.423 r_dihedral_angle_4_deg 19.223 r_dihedral_angle_3_deg 18.116 r_dihedral_angle_1_deg 7.132 r_mcangle_it 4.314 r_mcbond_it 2.855 r_mcbond_other 2.855 r_angle_refined_deg 1.848 r_angle_other_deg 1.185 r_chiral_restr 0.108 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.005 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6348 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 100
Software Software Software Name Purpose XDS data reduction Aimless data scaling PDB_EXTRACT data extraction PHASER phasing REFMAC refinement GDA data reduction