9F2G

Crystal structure of SARS-CoV-2 N-protein C-terminal domain (apo form)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7CE0Chain A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5291PEG 3350 37%, 0.1 M Tris pH 8.5, 50 mM ammonium sulfate and 1 mM InsP6. Protein:precipitant ratio 1:1. Protein concentration: 16.5 mg/ml. Protein buffer: 20 mM Tris pH 8.0 and 150 mM NaCl.
Crystal Properties
Matthews coefficientSolvent content
2.1943.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.704α = 90
b = 45.14β = 93.96
c = 109.061γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKB mirrors, rectangular beam shape2021-05-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979260ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)CC (Half)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
11.5748.4297.40.0190.99921.26.412314119.806
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.571.674.10.5310.6471.24.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.5748.42116789633797.390.190930.188870.22854RANDOM23.748
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]
0.3-0.320.73-0.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.708
r_dihedral_angle_1_deg6.549
r_long_range_B_refined6.292
r_long_range_B_other6.13
r_dihedral_angle_2_deg5.822
r_scangle_other4.658
r_scbond_it3.042
r_scbond_other3.042
r_mcangle_it2.937
r_mcangle_other2.937
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.708
r_dihedral_angle_1_deg6.549
r_long_range_B_refined6.292
r_long_range_B_other6.13
r_dihedral_angle_2_deg5.822
r_scangle_other4.658
r_scbond_it3.042
r_scbond_other3.042
r_mcangle_it2.937
r_mcangle_other2.937
r_mcbond_it2.041
r_mcbond_other2.041
r_angle_refined_deg1.531
r_angle_other_deg0.51
r_chiral_restr0.077
r_gen_planes_refined0.009
r_bond_refined_d0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 AtomsNumber
Protein Atoms6974
Nucleic Acid Atoms
Solvent Atoms1041
Heterogen Atoms55

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
BUCCANEERmodel building
Cootmodel building
PDB_EXTRACTdata extraction