6ZCO

Crystal Structure of C-terminal Dimerization Domain of Nucleocapsid Phosphoprotein from SARS-CoV-2, crystal form II


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION277tba
Crystal Properties
Matthews coefficientSolvent content
2.7555.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.203α = 90
b = 88.203β = 90
c = 42.763γ = 90
Symmetry
Space GroupI 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-06-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.000SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.3644.09697.80.0410.0470.01620.27.634588
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.3611.4386.61.0931.0931.4460.6980.73.5

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 REPLACEMENTTHROUGHOUT6yun1.3613032473170996.810.15170.14950.1962RANDOM28.894
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]
-1.14-1.142.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.809
r_sphericity_free26.737
r_dihedral_angle_4_deg17.93
r_dihedral_angle_3_deg13.639
r_sphericity_bonded12.693
r_dihedral_angle_1_deg6.069
r_rigid_bond_restr3.06
r_angle_refined_deg1.645
r_angle_other_deg1.023
r_chiral_restr0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.809
r_sphericity_free26.737
r_dihedral_angle_4_deg17.93
r_dihedral_angle_3_deg13.639
r_sphericity_bonded12.693
r_dihedral_angle_1_deg6.069
r_rigid_bond_restr3.06
r_angle_refined_deg1.645
r_angle_other_deg1.023
r_chiral_restr0.11
r_bond_refined_d0.016
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms936
Nucleic Acid Atoms
Solvent Atoms153
Heterogen Atoms

Software

Software
Software NamePurpose
XDSdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHENIXphasing