7TX3

Neutron crystal structure of SARS-CoV-2 NSP3 macrodomain at 293 K (P43 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 DROP9.5293100 mM CHES pH 9.5, 34% PEG 3000
Crystal Properties
Matthews coefficientSolvent content
2.2144.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.328α = 90
b = 89.328β = 90
c = 40.349γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS EIGER R 4MOSMIC VARIMAX2021-03-29MSINGLE WAVELENGTH
21neutron293AREA DETECTORORNL ANGER CAMERACOLLIMATORS2021-03-15LLAUE
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
11.628.3999.60.0870.0380.99615.65.942240
21.8914.12940.2170.1010.9267.24.424142
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)
11.61.630.2650.8744.62.8
21.891.960.25240.4112.73.1

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 REPLACEMENT1.623.1442212204299.630.12390.1576RANDOM22.64
NEUTRON DIFFRACTIONMOLECULAR REPLACEMENT1.8914.1224141117394.010.22580.275RANDOM22.64
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_d20.8052
f_dihedral_angle_d20.8052
f_angle_d1.474
f_angle_d1.474
f_chiral_restr0.0809
f_chiral_restr0.0809
f_bond_d0.0119
f_bond_d0.0119
f_plane_restr0.0092
f_plane_restr0.0092
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2535
Nucleic Acid Atoms
Solvent Atoms322
Heterogen Atoms13

Software

Software
Software NamePurpose
PHENIXrefinement
Mantiddata reduction
LAUENORMdata scaling
PHASERphasing
Cootmodel building