7QT5

Room temperature In-situ SARS-CoV-2 MPRO with bound Z31792168


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.529311% (v/v) PEG 4K, 5% (v/v) DMSO, 0.1 M MES pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.0640.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.773α = 90
b = 54.595β = 101.481
c = 45.313γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELDECTRIS PILATUS 6M-F2020-05-19MSINGLE 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
12.2644.4298.61.70.1840.0670.9949.9712834
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)
12.262.3499.61.9562.110.7670.4257

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-VALUE7AEH2.2644.421283364698.5640.1710.16760.231348.917
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]
-0.795-0.9470.7130.431
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.284
r_dihedral_angle_3_deg17.725
r_dihedral_angle_4_deg14.907
r_dihedral_angle_1_deg8.351
r_lrange_other5.197
r_lrange_it5.166
r_scangle_it3.408
r_scangle_other3.407
r_mcangle_it2.866
r_mcangle_other2.865
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.284
r_dihedral_angle_3_deg17.725
r_dihedral_angle_4_deg14.907
r_dihedral_angle_1_deg8.351
r_lrange_other5.197
r_lrange_it5.166
r_scangle_it3.408
r_scangle_other3.407
r_mcangle_it2.866
r_mcangle_other2.865
r_scbond_it2.174
r_scbond_other2.173
r_mcbond_other1.847
r_mcbond_it1.846
r_angle_refined_deg1.691
r_angle_other_deg1.314
r_xyhbond_nbd_refined0.205
r_nbd_refined0.199
r_symmetry_nbd_other0.189
r_nbtor_refined0.17
r_symmetry_xyhbond_nbd_refined0.167
r_nbd_other0.163
r_symmetry_nbd_refined0.155
r_symmetry_nbtor_other0.078
r_chiral_restr0.073
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_symmetry_xyhbond_nbd_other0.007
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2325
Nucleic Acid Atoms
Solvent Atoms25
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing