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Crystal structure of HLA-A*11:01 in complex with KRAS peptide (VVVGAGGVGK)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HN7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Ammonium sulfate, 0.1 M Sodium cacodylate pH 6, 25% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.57 52.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.854 α = 90 b = 117.028 β = 99.3 c = 110.643 γ = 90
Symmetry Space Group P 1 21 1
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 DECTRIS PILATUS3 6M 2017-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.46 79.96 99.9 0.189 0.204 0.074 0.99 9.3 7.5 65854
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.46 2.5 100 1.147 1.231 0.44 0.562 2 7.8
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 2HN7 2.46 79.96 62612 3237 99.9 0.2296 0.22804 0.236 0.25954 0.2691 RANDOM 35.28
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] 1.83 -2.75 0.3 -1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.746 r_dihedral_angle_4_deg 18.831 r_dihedral_angle_3_deg 16.026 r_dihedral_angle_1_deg 7.585 r_long_range_B_refined 2.929 r_long_range_B_other 2.926 r_angle_refined_deg 1.686 r_scangle_other 1.465 r_mcangle_it 1.353 r_mcangle_other 1.353
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.746 r_dihedral_angle_4_deg 18.831 r_dihedral_angle_3_deg 16.026 r_dihedral_angle_1_deg 7.585 r_long_range_B_refined 2.929 r_long_range_B_other 2.926 r_angle_refined_deg 1.686 r_scangle_other 1.465 r_mcangle_it 1.353 r_mcangle_other 1.353 r_angle_other_deg 1.244 r_scbond_it 0.852 r_scbond_other 0.852 r_mcbond_it 0.771 r_mcbond_other 0.771 r_chiral_restr 0.075 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 12518 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing