7BF4

Crystal structure of SARS-CoV-2 macrodomain in complex with GMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6YWK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.3293.1530% PEG 4000, 0.2 M sodium acetate, 0.1 MgCl2, 0.1 M tris, pH 8.3
Crystal Properties
Matthews coefficientSolvent content
2.3547.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.529α = 90
b = 72.529β = 90
c = 33.346γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2020-06-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.00003SLSX06DA

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
11.5536.2699.20.0640.0760.030.99813.86.125315
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)
11.551.692.80.3490.4550.2440.8072.63.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT6ywk1.5536.2624080122299.080.14010.13840.1743RANDOM16.024
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]
0.140.14-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.67
r_dihedral_angle_4_deg13.095
r_dihedral_angle_3_deg11.851
r_dihedral_angle_1_deg6.881
r_angle_refined_deg1.686
r_angle_other_deg1.549
r_chiral_restr0.104
r_bond_refined_d0.018
r_gen_planes_refined0.013
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.67
r_dihedral_angle_4_deg13.095
r_dihedral_angle_3_deg11.851
r_dihedral_angle_1_deg6.881
r_angle_refined_deg1.686
r_angle_other_deg1.549
r_chiral_restr0.104
r_bond_refined_d0.018
r_gen_planes_refined0.013
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1285
Nucleic Acid Atoms
Solvent Atoms205
Heterogen Atoms84

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing