7HUD

PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment B08 from the F2X-Entry Screen in monoclinic space group


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6Y2E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.72910.2 M MIB (sodium malonate, imidazole, and boric acid in the molar ratios 2:3:3) pH 7.7, 23.5 % PEG 1500, 5 % DMSO, 1 mM DTT. Crystal seeds were used to ensure reproducible crystal growth.
Crystal Properties
Matthews coefficientSolvent content
1.935

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.55α = 90
b = 52.81β = 102.65
c = 44.69γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2022-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.9184BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
11.6147.6499.60.0870.0960.999000000000000112.1633149
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.611.7199.21.7681.94099999999999980.363

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.6147.6431490165899.650.20060.199080.22864RANDOM27.876
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]
1.63-0.86-0.18-0.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.107
r_dihedral_angle_3_deg14.807
r_dihedral_angle_4_deg12.542
r_dihedral_angle_1_deg7.779
r_long_range_B_other6.21
r_long_range_B_refined6.209
r_scangle_other4.793
r_mcangle_it3.162
r_mcangle_other3.162
r_scbond_it3.094
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.107
r_dihedral_angle_3_deg14.807
r_dihedral_angle_4_deg12.542
r_dihedral_angle_1_deg7.779
r_long_range_B_other6.21
r_long_range_B_refined6.209
r_scangle_other4.793
r_mcangle_it3.162
r_mcangle_other3.162
r_scbond_it3.094
r_scbond_other3.093
r_mcbond_it2.235
r_mcbond_other2.234
r_angle_refined_deg1.527
r_angle_other_deg1.406
r_chiral_restr0.076
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2367
Nucleic Acid Atoms
Solvent Atoms74
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing