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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 10% PEG 6000, 10mM magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.54 51.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.98 α = 90 b = 81.23 β = 90 c = 110.47 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 PSI PILATUS 6M mirrors 2012-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
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 1.77 81.23 100 0.09 0.035 0.999 17.7 7.3 45559
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 1.77 1.82 100 0.752 0.296 0.803 2.8 7.4 3321
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 1.77 81.23 45492 2299 99.98 0.1655 0.1637 0.1743 0.199 0.2013 RANDOM 22.483
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] -0.01 0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.754 r_dihedral_angle_4_deg 20.58 r_dihedral_angle_3_deg 14.654 r_dihedral_angle_1_deg 6.067 r_angle_refined_deg 2.04 r_mcangle_it 1.78 r_mcbond_it 1.124 r_mcbond_other 1.124 r_angle_other_deg 0.937 r_chiral_restr 0.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.754 r_dihedral_angle_4_deg 20.58 r_dihedral_angle_3_deg 14.654 r_dihedral_angle_1_deg 6.067 r_angle_refined_deg 2.04 r_mcangle_it 1.78 r_mcbond_it 1.124 r_mcbond_other 1.124 r_angle_other_deg 0.937 r_chiral_restr 0.118 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3179 Nucleic Acid Atoms Solvent Atoms 295 Heterogen Atoms 60
Software Software Software Name Purpose XDS data reduction Aimless data scaling PDB_EXTRACT data extraction PHASER phasing REFMAC refinement GDA data reduction