5S74

PanDDA analysis group deposition of ground-state model of SARS-CoV-2 Nsp3 macrodomain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP0.1293.1530% PEG 3K
Crystal Properties
Matthews coefficientSolvent content
2.0540.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.877α = 90
b = 87.877β = 90
c = 38.634γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-05-21SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91188DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
10.9562.2780.80.07419.1138299
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
10.950.977.41.2260.33685

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 SYNTHESISTHROUGHOUT6WOJ0.9662.22138299701981.80.17690.17650.1852RANDOM12.467
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]
-0.33-0.330.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.177
r_dihedral_angle_4_deg22.812
r_dihedral_angle_3_deg11.353
r_dihedral_angle_1_deg6.857
r_angle_refined_deg1.838
r_mcangle_it1.778
r_angle_other_deg1.666
r_mcbond_it1.224
r_mcbond_other1.223
r_chiral_restr0.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.177
r_dihedral_angle_4_deg22.812
r_dihedral_angle_3_deg11.353
r_dihedral_angle_1_deg6.857
r_angle_refined_deg1.838
r_mcangle_it1.778
r_angle_other_deg1.666
r_mcbond_it1.224
r_mcbond_other1.223
r_chiral_restr0.095
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2526
Nucleic Acid Atoms
Solvent Atoms338
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing