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Newly identified epitope N1 derived from SARS-CoV N protein complexed with HLA-A*2402
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BCK PDB ENTRY 2BCK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.9 277 0.2M Ammonium sulfate, 0.1M Tris pH 8.9, 25% w/v Polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.13 60.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.422 α = 90 b = 85.823 β = 90 c = 92.221 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 IMAGE PLATE RIGAKU RAXIS VII 2008-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.4 28.94 98.6 0.099 0.099 40.671 6.7 22272 3 3 43.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.4 2.49 97.5 0.387 0.387 6.211 6.8 2166
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 PDB ENTRY 2BCK 2.4 28.94 21091 1138 98.68 0.21669 0.213 0.2102 0.284 0.2806 RANDOM 43.465
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] -0.04 -0.12 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.723 r_dihedral_angle_4_deg 21.739 r_dihedral_angle_3_deg 18.555 r_dihedral_angle_1_deg 6.267 r_scangle_it 2.995 r_scbond_it 1.828 r_mcangle_it 1.447 r_angle_refined_deg 1.443 r_mcbond_it 0.842 r_symmetry_hbond_refined 0.352
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.723 r_dihedral_angle_4_deg 21.739 r_dihedral_angle_3_deg 18.555 r_dihedral_angle_1_deg 6.267 r_scangle_it 2.995 r_scbond_it 1.828 r_mcangle_it 1.447 r_angle_refined_deg 1.443 r_mcbond_it 0.842 r_symmetry_hbond_refined 0.352 r_nbtor_refined 0.298 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.2 r_xyhbond_nbd_refined 0.171 r_chiral_restr 0.096 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3136 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling