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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 Sodium Cacodylate, pH 6, 15% PEG 8000, 15% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.68 54.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.27 α = 91.37 b = 49.13 β = 93.57 c = 107.46 γ = 95.75
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 2.09 48.86 97.5 0.098 0.087 0.983 4.8 2 54249
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 2.09 2.14 95.7 0.358 0.317 0.822 2 2 3935
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4I4W 2.09 48.86 54207 2757 97.48 0.1783 0.1756 0.2263 0.2447 RANDOM 51.539
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] 0.13 0.2 -0.05 -0.95 0.52 0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.367 r_dihedral_angle_4_deg 17.379 r_dihedral_angle_3_deg 16.547 r_dihedral_angle_1_deg 7.254 r_mcangle_it 2.041 r_angle_refined_deg 1.857 r_mcbond_it 1.238 r_mcbond_other 1.238 r_angle_other_deg 0.92 r_chiral_restr 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.367 r_dihedral_angle_4_deg 17.379 r_dihedral_angle_3_deg 16.547 r_dihedral_angle_1_deg 7.254 r_mcangle_it 2.041 r_angle_refined_deg 1.857 r_mcbond_it 1.238 r_mcbond_other 1.238 r_angle_other_deg 0.92 r_chiral_restr 0.11 r_bond_refined_d 0.017 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 6366 Nucleic Acid Atoms Solvent Atoms 497 Heterogen Atoms 77
Software Software Software Name Purpose XDS data reduction Aimless data scaling PDB_EXTRACT data extraction PHASER phasing REFMAC refinement GDA data reduction