7QT8

Room temperature In-situ SARS-CoV-2 MPRO with bound ABT-957


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
2.141.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.245α = 90
b = 54.673β = 100.385
c = 116.578γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELDECTRIS PILATUS 6M-F2020-07-02MSINGLE 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
12.0149.3795.20.170.1840.0670.9949.9737088
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)
12.012.0899.61.9562.110.7670.4257

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-VALUE7AEH2.0149.3737088180498.6440.2050.20370.236534.315
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]
1.078-0.5810.342-1.132
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.302
r_dihedral_angle_4_deg24.127
r_dihedral_angle_3_deg15.924
r_dihedral_angle_other_3_deg12.095
r_dihedral_angle_1_deg7.866
r_lrange_it3.507
r_lrange_other3.502
r_scangle_it2.283
r_scangle_other2.282
r_angle_refined_deg1.752
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.302
r_dihedral_angle_4_deg24.127
r_dihedral_angle_3_deg15.924
r_dihedral_angle_other_3_deg12.095
r_dihedral_angle_1_deg7.866
r_lrange_it3.507
r_lrange_other3.502
r_scangle_it2.283
r_scangle_other2.282
r_angle_refined_deg1.752
r_mcangle_it1.639
r_mcangle_other1.639
r_angle_other_deg1.385
r_scbond_it1.352
r_scbond_other1.352
r_mcbond_it0.967
r_mcbond_other0.967
r_nbd_other0.249
r_symmetry_nbd_refined0.236
r_nbd_refined0.207
r_symmetry_nbd_other0.187
r_nbtor_refined0.17
r_xyhbond_nbd_refined0.128
r_chiral_restr0.118
r_symmetry_xyhbond_nbd_refined0.103
r_symmetry_nbtor_other0.084
r_ncsr_local_group_10.076
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4695
Nucleic Acid Atoms
Solvent Atoms48
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing