7TX4

Neutron crystal structure of SARS-CoV-2 NSP3 macrodomain at 293 K (P21 crystal form)


X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7KQO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5289100 mM MES pH 6.5, 28% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.1442.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.681α = 90
b = 33.817β = 98.3
c = 61.697γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS EIGER R 4MOSMIC VARIMAX2021-04-20MSINGLE WAVELENGTH
21neutron293AREA DETECTORORNL ANGER CAMERACOLLIMATORS2021-04-20LLAUE
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54
2SPALLATION SOURCEORNL Spallation Neutron Source BEAMLINE MANDI2.00-4.00ORNL Spallation Neutron SourceMANDI

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)R Split (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
11.961.0596.60.0970.0450.98915.25.911968
22.3513.7286.70.1820.080.91416.95.25663
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.970.4520.8233.26.1
22.352.430.3640.5565.34.2

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT1.925.491196060796.630.16620.224RANDOM26.88
NEUTRON DIFFRACTIONMOLECULAR REPLACEMENT2.3512.75566029086.440.17680.2595RANDOM26.88
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d20.7608
f_dihedral_angle_d20.7608
f_angle_d1.2016
f_angle_d1.2016
f_chiral_restr0.0622
f_chiral_restr0.0622
f_bond_d0.0086
f_bond_d0.0086
f_plane_restr0.0054
f_plane_restr0.0054
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1263
Nucleic Acid Atoms
Solvent Atoms110
Heterogen Atoms

Software

Software
Software NamePurpose
PHENIXrefinement
Mantiddata reduction
LAUENORMdata scaling
PHASERphasing
Cootmodel building