7QT7

Room temperature In-situ SARS-CoV-2 MPRO with bound Z4439011520


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7AEH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.529811% (v/v) PEG 4K, 5% (v/v) DMSO, 0.1 M MES pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.0740.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.692α = 90
b = 54.474β = 101.698
c = 45.251γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELDECTRIS PILATUS 6M-F2020-05-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I241.0DiamondI24

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
12.2544.3595.20.1620.1740.0610.9878.97.212607
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)
12.252.331.5381.6520.5770.3111.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7AEH2.2544.351260461895.1460.1650.16290.216347.168
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]
0.392-0.3450.252-0.461
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.119
r_dihedral_angle_4_deg16.042
r_dihedral_angle_3_deg15.811
r_dihedral_angle_1_deg7.883
r_dihedral_angle_other_2_deg7.052
r_lrange_other5.127
r_lrange_it5.126
r_scangle_it3.428
r_scangle_other3.427
r_mcangle_it2.668
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.119
r_dihedral_angle_4_deg16.042
r_dihedral_angle_3_deg15.811
r_dihedral_angle_1_deg7.883
r_dihedral_angle_other_2_deg7.052
r_lrange_other5.127
r_lrange_it5.126
r_scangle_it3.428
r_scangle_other3.427
r_mcangle_it2.668
r_mcangle_other2.668
r_scbond_it2.239
r_scbond_other2.239
r_angle_refined_deg1.81
r_mcbond_it1.719
r_mcbond_other1.716
r_angle_other_deg1.34
r_symmetry_nbd_refined0.289
r_chiral_restr0.284
r_nbd_refined0.209
r_nbd_other0.203
r_symmetry_nbd_other0.19
r_nbtor_refined0.175
r_symmetry_xyhbond_nbd_refined0.173
r_xyhbond_nbd_refined0.154
r_symmetry_nbtor_other0.085
r_dihedral_angle_other_3_deg0.032
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2328
Nucleic Acid Atoms
Solvent Atoms25
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing