7QT6

Room temperature In-situ SARS-CoV-2 MPRO with bound Z1367324110


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
2.0840.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.212α = 90
b = 54.779β = 101.235
c = 45.336γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELDECTRIS PILATUS 6M-F2020-05-13MSINGLE 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
12.1149.3199.70.170.1790.0530.9967.99.816050
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)
12.112.192.4292.5510.7550.3311.2

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-VALUE7AEH2.1144.5061604980899.6960.1790.17710.222151.605
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]
-0.105-0.357-0.2930.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.974
r_dihedral_angle_4_deg19.364
r_dihedral_angle_3_deg15.965
r_dihedral_angle_1_deg8.189
r_lrange_it5.77
r_lrange_other5.761
r_scangle_it3.716
r_scangle_other3.715
r_mcangle_other2.931
r_mcangle_it2.929
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.974
r_dihedral_angle_4_deg19.364
r_dihedral_angle_3_deg15.965
r_dihedral_angle_1_deg8.189
r_lrange_it5.77
r_lrange_other5.761
r_scangle_it3.716
r_scangle_other3.715
r_mcangle_other2.931
r_mcangle_it2.929
r_scbond_other2.306
r_scbond_it2.304
r_angle_refined_deg1.843
r_mcbond_it1.831
r_mcbond_other1.811
r_angle_other_deg1.384
r_nbd_other0.293
r_symmetry_nbd_refined0.226
r_nbd_refined0.207
r_symmetry_nbd_other0.203
r_nbtor_refined0.175
r_xyhbond_nbd_refined0.173
r_symmetry_nbtor_other0.087
r_symmetry_xyhbond_nbd_refined0.087
r_chiral_restr0.073
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2324
Nucleic Acid Atoms
Solvent Atoms25
Heterogen Atoms19

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing