3I6L

Newly identified epitope N1 derived from SARS-CoV N protein complexed with HLA-A*2402


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BCKPDB ENTRY 2BCK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.92770.2M Ammonium sulfate, 0.1M Tris pH 8.9, 25% w/v Polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.1360.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.422α = 90
b = 85.823β = 90
c = 92.221γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS VII2008-06-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54178

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.428.9498.60.0990.09940.6716.7222723343.5
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)RedundancyNumber Unique Reflections (All)
2.42.4997.50.3870.3876.2116.82166

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2BCK2.428.9421091113898.680.216690.2130.284RANDOM43.465
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]
-0.04-0.120.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.723
r_dihedral_angle_4_deg21.739
r_dihedral_angle_3_deg18.555
r_dihedral_angle_1_deg6.267
r_scangle_it2.995
r_scbond_it1.828
r_mcangle_it1.447
r_angle_refined_deg1.443
r_mcbond_it0.842
r_symmetry_hbond_refined0.352
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.723
r_dihedral_angle_4_deg21.739
r_dihedral_angle_3_deg18.555
r_dihedral_angle_1_deg6.267
r_scangle_it2.995
r_scbond_it1.828
r_mcangle_it1.447
r_angle_refined_deg1.443
r_mcbond_it0.842
r_symmetry_hbond_refined0.352
r_nbtor_refined0.298
r_nbd_refined0.215
r_symmetry_vdw_refined0.2
r_xyhbond_nbd_refined0.171
r_chiral_restr0.096
r_bond_refined_d0.013
r_gen_planes_refined0.005
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 AtomsNumber
Protein Atoms3136
Nucleic Acid Atoms
Solvent Atoms242
Heterogen Atoms

Software

Software
Software NamePurpose
CrystalCleardata collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling