7QT9

Room temperature In-situ SARS-CoV-2 MPRO with bound Z4439011584


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
2.0740.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.199α = 90
b = 54.485β = 101.092
c = 115.725γ = 90
Symmetry
Space GroupI 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)R Sym I (Observed)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
12.4356.84697.90.1660.1830.0730.98710.85.910345
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)
12.432.5297.71.2411.380.5780.3055.9

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-VALUE7AEH2.4356.8461033954397.870.1520.14960.200345.722
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]
-0.6090.211-0.5490.998
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35
r_dihedral_angle_3_deg15.818
r_dihedral_angle_4_deg14.355
r_dihedral_angle_other_2_deg8.494
r_dihedral_angle_1_deg8.161
r_lrange_it5.563
r_lrange_other5.562
r_scangle_it4.01
r_scangle_other4.009
r_mcangle_other2.913
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35
r_dihedral_angle_3_deg15.818
r_dihedral_angle_4_deg14.355
r_dihedral_angle_other_2_deg8.494
r_dihedral_angle_1_deg8.161
r_lrange_it5.563
r_lrange_other5.562
r_scangle_it4.01
r_scangle_other4.009
r_mcangle_other2.913
r_mcangle_it2.912
r_scbond_it2.483
r_scbond_other2.482
r_angle_refined_deg1.903
r_mcbond_it1.831
r_mcbond_other1.826
r_angle_other_deg1.359
r_nbd_other0.27
r_symmetry_nbd_refined0.227
r_nbd_refined0.211
r_symmetry_nbd_other0.193
r_nbtor_refined0.178
r_xyhbond_nbd_refined0.162
r_symmetry_xyhbond_nbd_refined0.117
r_symmetry_nbtor_other0.085
r_chiral_restr0.076
r_dihedral_angle_other_3_deg0.055
r_bond_refined_d0.013
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 Atoms2347
Nucleic Acid Atoms
Solvent Atoms23
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing