7H0C

Crystal structure of SARS-CoV-2 NSP3 Macrodomain in complex with ASAP-0012349-001


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
2.0740.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.167α = 90
b = 32.962β = 94.35
c = 120.909γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 9M2023-07-07SINGLE 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
11.4360.18990.160.1750.0680.9948.16.455550
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)
11.431.4591.62.1942.481.1350.2944.7

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 REPLACEMENTTHROUGHOUT1.42920.7255352274298.50.18570.18430.2121RANDOM21.7
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]
3.19334.12792.0767-5.2699
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion15.99
t_omega_torsion4.17
t_angle_deg1.07
t_bond_d0.011
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 Atoms2535
Nucleic Acid Atoms
Solvent Atoms433
Heterogen Atoms62

Software

Software
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction