5SM8

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z2027158783


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
2.6754.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.586α = 90
b = 68.023β = 90
c = 138.519γ = 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
11.95138.51000.2440.2650.1010.9795.36.847406
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)
11.95299.44.4474.8391.8940.3086.43302

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 SYNTHESISTHROUGHOUT7QGI1.9569.2642975220595.380.22610.22390.2672RANDOM45.795
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]
-0.154.04-3.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.877
r_dihedral_angle_4_deg16.932
r_dihedral_angle_3_deg15.569
r_dihedral_angle_1_deg8.14
r_mcangle_it6.818
r_mcbond_it4.397
r_mcbond_other4.386
r_angle_refined_deg1.573
r_angle_other_deg1.331
r_chiral_restr0.072
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.877
r_dihedral_angle_4_deg16.932
r_dihedral_angle_3_deg15.569
r_dihedral_angle_1_deg8.14
r_mcangle_it6.818
r_mcbond_it4.397
r_mcbond_other4.386
r_angle_refined_deg1.573
r_angle_other_deg1.331
r_chiral_restr0.072
r_bond_refined_d0.009
r_gen_planes_refined0.008
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 Atoms431
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing