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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 2.56 51.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.06 α = 90 b = 81.34 β = 90 c = 110.93 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 2012-06-30 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 1.18 55.47 99.1 0.053 0.022 0.999 17.5 7.1 150669
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 1.18 1.21 96 0.721 0.294 0.823 3 6.8 10692
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 1.18 55.47 150583 7561 99 0.1631 0.1622 0.1802 0.1956 RANDOM 18.044
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] -0.02 -0.07 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.337 r_dihedral_angle_4_deg 20.17 r_dihedral_angle_3_deg 13.305 r_dihedral_angle_1_deg 6.583 r_angle_refined_deg 2.438 r_mcangle_it 1.575 r_mcbond_it 1.045 r_mcbond_other 1.045 r_angle_other_deg 1.026 r_chiral_restr 0.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.337 r_dihedral_angle_4_deg 20.17 r_dihedral_angle_3_deg 13.305 r_dihedral_angle_1_deg 6.583 r_angle_refined_deg 2.438 r_mcangle_it 1.575 r_mcbond_it 1.045 r_mcbond_other 1.045 r_angle_other_deg 1.026 r_chiral_restr 0.134 r_bond_refined_d 0.024 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3173 Nucleic Acid Atoms Solvent Atoms 555 Heterogen Atoms 128
Software Software Software Name Purpose XDS data reduction Aimless data scaling PDB_EXTRACT data extraction PHASER phasing REFMAC refinement GDA data reduction