5SME

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z437584380


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
2.6753.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.707α = 90
b = 67.862β = 90
c = 138.4γ = 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
11.91138.4199.90.2220.240.0920.9946.66.850356
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)
11.911.9598.83.6113.9131.4930.3616.83342

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 SYNTHESISTHROUGHOUT7QGI1.9169.247657245499.590.21470.21260.2553RANDOM41.363
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]
-1.084.56-3.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.717
r_dihedral_angle_4_deg19.295
r_dihedral_angle_3_deg15.704
r_dihedral_angle_1_deg7.667
r_mcangle_it5.056
r_mcbond_it3.183
r_mcbond_other3.183
r_angle_refined_deg1.439
r_angle_other_deg1.287
r_chiral_restr0.067
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.717
r_dihedral_angle_4_deg19.295
r_dihedral_angle_3_deg15.704
r_dihedral_angle_1_deg7.667
r_mcangle_it5.056
r_mcbond_it3.183
r_mcbond_other3.183
r_angle_refined_deg1.439
r_angle_other_deg1.287
r_chiral_restr0.067
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 Atoms3684
Nucleic Acid Atoms
Solvent Atoms427
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing