5SLK

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z1354370680


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62781.26 M sodium phosphate monobasic, 0.14 M potassium phosphate dibasic
Crystal Properties
Matthews coefficientSolvent content
2.6653.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.596α = 90
b = 67.536β = 90
c = 138.752γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2022-02-03SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91788DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.21138.7699.90.2740.2970.1130.9885.26.732615
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.212.2898.83.5553.841.440.29272774

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT7QGI2.2169.3830804153399.190.22350.22030.2846RANDOM56.434
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]
-1.495.58-4.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.106
r_dihedral_angle_4_deg17.172
r_dihedral_angle_3_deg16.969
r_dihedral_angle_1_deg8.245
r_mcangle_it7.345
r_mcbond_it4.632
r_mcbond_other4.631
r_angle_refined_deg1.448
r_angle_other_deg1.233
r_chiral_restr0.062
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.106
r_dihedral_angle_4_deg17.172
r_dihedral_angle_3_deg16.969
r_dihedral_angle_1_deg8.245
r_mcangle_it7.345
r_mcbond_it4.632
r_mcbond_other4.631
r_angle_refined_deg1.448
r_angle_other_deg1.233
r_chiral_restr0.062
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3666
Nucleic Acid Atoms
Solvent Atoms427
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing