8ZFV | pdb_00008zfv

Crystal Structure of C-terminal domain of nucleocapsid protein from SARS-CoV-2 in complex with ceftriaxone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6YUN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29330% PEG4000, 0.2 M Lithium sulfate, 50 mM Tris pH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.6753.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.539α = 106.66
b = 46.643β = 90.11
c = 69.021γ = 93.46
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELRIGAKU HyPix-6000HE2022-08-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54184

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
1226.5899.20.99717.84.234801
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.050.8893.8

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6YUN226.5833047175299.180.150190.147310.15990.204940.2123RANDOM16.983
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]
-1.28-0.03-0.121.070.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg21.586
r_dihedral_angle_3_deg14.035
r_dihedral_angle_1_deg7.341
r_long_range_B_refined6.47
r_long_range_B_other6.47
r_scangle_other3.835
r_scbond_it2.365
r_scbond_other2.365
r_mcangle_it2.086
r_mcangle_other2.086
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg21.586
r_dihedral_angle_3_deg14.035
r_dihedral_angle_1_deg7.341
r_long_range_B_refined6.47
r_long_range_B_other6.47
r_scangle_other3.835
r_scbond_it2.365
r_scbond_other2.365
r_mcangle_it2.086
r_mcangle_other2.086
r_angle_refined_deg1.844
r_mcbond_it1.295
r_mcbond_other1.29
r_angle_other_deg0.662
r_chiral_restr0.551
r_bond_refined_d0.008
r_gen_planes_refined0.008
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 Atoms3548
Nucleic Acid Atoms
Solvent Atoms669
Heterogen Atoms120

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing