7TX5

Neutron crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at 293 K (C2 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, 25% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.5351.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 132.808α = 90
b = 36.653β = 98.09
c = 38.233γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS EIGER R 4MOSMIC VARIMAX2021-08-30MSINGLE WAVELENGTH
21neutron293AREA DETECTORORNL ANGER CAMERACOLLIMATORS2021-08-30LLAUE
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54
2SPALLATION SOURCEORNL High Flux Isotope Reactor BEAMLINE CG4D3.3-4.5ORNL High Flux Isotope ReactorCG4D

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
11.9565.7492.90.070.0360.99219.25.612576
22.335.0775.40.1510.1180.9544.446252
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)
11.952.020.2360.95465.3
22.32.40.2810.613.24.4

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 REPLACEMENT1.9528.121257260892.890.13220.1719RANDOM33.44
NEUTRON DIFFRACTIONMOLECULAR REPLACEMENT2.332.87625033075.110.18730.2592RANDOM33.44
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_d22.5981
f_dihedral_angle_d22.5981
f_angle_d1.3541
f_angle_d1.3541
f_chiral_restr0.0653
f_chiral_restr0.0653
f_bond_d0.0099
f_bond_d0.0099
f_plane_restr0.0062
f_plane_restr0.0062
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1256
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms36

Software

Software
Software NamePurpose
PHENIXrefinement
Cootmodel building
PHASERphasing