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Crystal structure of the SLA-1*0808 allele and ASFV antigenic peptide at 1.8 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5H94
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.2 M Sodium thiocyanate,20% w/v Polyethylene glycol 3,350,pH 6.9
Crystal Properties Matthews coefficient Solvent content 2.33 47.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.538 α = 90 b = 50.08 β = 101.38 c = 53.835 γ = 90
Symmetry Space Group C 1 2 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 2023-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.987 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.56 50 96.9 0.124 14.667 2.3 56188
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.56 1.59 1.302
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.56 47.65 48612 2603 88.16 0.21037 0.20889 0.2187 0.23832 0.2458 RANDOM 19.434
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 -0.17 -0.07 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.344 r_dihedral_angle_4_deg 16.652 r_dihedral_angle_3_deg 15.002 r_dihedral_angle_1_deg 7.139 r_long_range_B_refined 6.366 r_long_range_B_other 6.342 r_scangle_other 4.196 r_mcangle_it 3.647 r_mcangle_other 3.646 r_scbond_it 2.616
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.344 r_dihedral_angle_4_deg 16.652 r_dihedral_angle_3_deg 15.002 r_dihedral_angle_1_deg 7.139 r_long_range_B_refined 6.366 r_long_range_B_other 6.342 r_scangle_other 4.196 r_mcangle_it 3.647 r_mcangle_other 3.646 r_scbond_it 2.616 r_scbond_other 2.615 r_mcbond_other 2.185 r_mcbond_it 2.184 r_angle_refined_deg 1.641 r_angle_other_deg 1.422 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 3105 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling HKL-3000 data reduction PHASER phasing