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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 PDB entry 4I4W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 291 22% PEG 4000 and 0.2 M ammonium sulphate, 0.1M sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.53 51.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51 α = 90 b = 81.44 β = 90 c = 110.06 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 2013-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.920 Diamond I04-1
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 1.59 55.03 99.9 0.073 0.029 0.999 16.5 7.3 62396
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 1.59 1.63 100 0.725 0.293 0.811 3 7 4555
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 PDB entry 4I4W 1.59 55.03 62324 3157 99.86 0.1654 0.1638 0.1766 0.1944 0.204 RANDOM 23.73
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 -0.19 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.404 r_dihedral_angle_4_deg 16.97 r_dihedral_angle_3_deg 14.798 r_dihedral_angle_1_deg 6.022 r_mcangle_it 1.98 r_angle_refined_deg 1.961 r_mcbond_other 1.271 r_mcbond_it 1.27 r_angle_other_deg 0.922 r_chiral_restr 0.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.404 r_dihedral_angle_4_deg 16.97 r_dihedral_angle_3_deg 14.798 r_dihedral_angle_1_deg 6.022 r_mcangle_it 1.98 r_angle_refined_deg 1.961 r_mcbond_other 1.271 r_mcbond_it 1.27 r_angle_other_deg 0.922 r_chiral_restr 0.127 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 3178 Nucleic Acid Atoms Solvent Atoms 314 Heterogen Atoms 62
Software Software Software Name Purpose Aimless data scaling PDB_EXTRACT data extraction PHASER phasing REFMAC refinement GDA data reduction