☰ Navigation Tabs
Crystal structure of HLA-A*11:01 in complex with KRAS G12D peptide (VVVGADGVGK)
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 Lithium sulfate, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3500
Crystal Properties Matthews coefficient Solvent content 2.54 51.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.224 α = 90 b = 121.432 β = 90 c = 127.863 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 DECTRIS PILATUS 6M-F 2018-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
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 1.81 88.05 100 0.26 0.269 0.069 0.998 8.7 15.1 166212
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 1.81 1.84 100 4.611 4.778 1.244 0.322 0.7 14.5
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 1.81 88.05 158094 8118 99.96 0.22111 0.21968 0.2253 0.24917 0.2544 RANDOM 26.136
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] 0.28 -0.73 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.672 r_dihedral_angle_4_deg 17.277 r_dihedral_angle_3_deg 13.468 r_dihedral_angle_1_deg 6.832 r_long_range_B_refined 4.528 r_long_range_B_other 4.424 r_scangle_other 1.712 r_angle_refined_deg 1.482 r_angle_other_deg 1.306 r_mcangle_it 1.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.672 r_dihedral_angle_4_deg 17.277 r_dihedral_angle_3_deg 13.468 r_dihedral_angle_1_deg 6.832 r_long_range_B_refined 4.528 r_long_range_B_other 4.424 r_scangle_other 1.712 r_angle_refined_deg 1.482 r_angle_other_deg 1.306 r_mcangle_it 1.274 r_mcangle_other 1.274 r_scbond_it 1.058 r_scbond_other 1.041 r_mcbond_it 0.749 r_mcbond_other 0.749 r_chiral_restr 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 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 12522 Nucleic Acid Atoms Solvent Atoms 1009 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing