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Conformational flexibility in HLA-B8: peptide tuning structural and dynamical changes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6P2S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 15% PEG4000, 0.1m citrate acid pH5.4, 0.2M ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.47 50.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.75 α = 90 b = 81.304 β = 90 c = 110.504 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 CCD AGILENT ATLAS CCD 2024-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE VMXi 0.976254 Diamond VMXi
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.27 65.49 100 0.114 0.997 7.3 7.1 77999
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.27 1.43 91.7 0.4834
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 6P2S 1.27 65.49 74060 3939 64.46 0.19823 0.19666 0.2065 0.22691 0.2367 RANDOM 22.972
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.634 r_long_range_B_other 9.044 r_long_range_B_refined 9.038 r_dihedral_angle_2_deg 7.45 r_dihedral_angle_1_deg 6.624 r_scangle_other 6.57 r_scbond_it 4.113 r_scbond_other 4.112 r_mcangle_it 3.868 r_mcangle_other 3.868
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.634 r_long_range_B_other 9.044 r_long_range_B_refined 9.038 r_dihedral_angle_2_deg 7.45 r_dihedral_angle_1_deg 6.624 r_scangle_other 6.57 r_scbond_it 4.113 r_scbond_other 4.112 r_mcangle_it 3.868 r_mcangle_other 3.868 r_mcbond_it 2.428 r_mcbond_other 2.428 r_angle_refined_deg 1.729 r_angle_other_deg 0.637 r_chiral_restr 0.097 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3060 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing XDS data scaling