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Crystal structure of HLA-C*07:02 in complex with RYR peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NT6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 0.1 M HEPES pH 8.5
2 mM ZnSO4
28 % jeffamine ED-2001 (Hampton)
Crystal Properties Matthews coefficient Solvent content 2.5 50.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.67 α = 90 b = 99.67 β = 90 c = 77.914 γ = 120
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 ADSC QUANTUM 210 2016-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.954 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.6 43.16 100 0.05 14.8 11.3 13655
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 4NT6 2.6 43.16 12942 698 99.96 0.16629 0.1632 0.1659 0.22082 0.2236 RANDOM 55.984
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] -27.78 -27.78 55.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.528 r_dihedral_angle_4_deg 16.947 r_dihedral_angle_3_deg 15.753 r_long_range_B_refined 7.512 r_long_range_B_other 7.511 r_dihedral_angle_1_deg 7.268 r_scangle_other 5.047 r_mcangle_it 4.92 r_mcangle_other 4.918 r_scbond_it 3.175
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.528 r_dihedral_angle_4_deg 16.947 r_dihedral_angle_3_deg 15.753 r_long_range_B_refined 7.512 r_long_range_B_other 7.511 r_dihedral_angle_1_deg 7.268 r_scangle_other 5.047 r_mcangle_it 4.92 r_mcangle_other 4.918 r_scbond_it 3.175 r_scbond_other 3.175 r_mcbond_it 3.152 r_mcbond_other 3.145 r_angle_refined_deg 1.384 r_angle_other_deg 0.941 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 3134 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing