7H06

Crystal structure of SARS-CoV-2 NSP3 Macrodomain in complex with ASAP-0010739-001


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.1 M MES (pH 6.50) and 30 % w/v PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.1843.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.26α = 90
b = 33.2β = 101.36
c = 63.99γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 9M2023-07-17SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9212DiamondI04-1

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
11.2435.4191.30.050.0550.0220.99914.15.341007
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)
11.241.2747.40.9291.2790.8740.3481.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.2435.4140990209791.10.17360.17290.1861RANDOM21.66
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]
1.74312.79321.6908-3.4339
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion15.24
t_omega_torsion4.97
t_angle_deg1.17
t_bond_d0.013
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1266
Nucleic Acid Atoms
Solvent Atoms247
Heterogen Atoms25

Software

Software
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction