5Y3Q

Crystal structure of SARS coronavirus papain-like protease conjugated with beta-mercaptoethanol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FE8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8295PEG3350, Bis-Tris propane/citric acid
Crystal Properties
Matthews coefficientSolvent content
2.6353.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 151.412α = 90
b = 33.264β = 125.01
c = 90.677γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2016-12-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A11NSRRCBL15A1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.6574.2799.70.041293.645072
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.7198.20.3473.63.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT2fe81.6574.2742759226699.450.148560.146670.18405RANDOM16.742
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]
0.010.1-0.190.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.517
r_sphericity_free21.895
r_dihedral_angle_3_deg13.144
r_dihedral_angle_4_deg10.705
r_sphericity_bonded6.168
r_dihedral_angle_1_deg5.611
r_long_range_B_refined2.93
r_long_range_B_other2.93
r_scangle_other1.513
r_mcangle_it1.485
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.517
r_sphericity_free21.895
r_dihedral_angle_3_deg13.144
r_dihedral_angle_4_deg10.705
r_sphericity_bonded6.168
r_dihedral_angle_1_deg5.611
r_long_range_B_refined2.93
r_long_range_B_other2.93
r_scangle_other1.513
r_mcangle_it1.485
r_mcangle_other1.484
r_angle_refined_deg1.258
r_scbond_it1.219
r_scbond_other1.219
r_rigid_bond_restr1.204
r_mcbond_it1.11
r_mcbond_other1.106
r_angle_other_deg0.865
r_chiral_restr0.072
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2498
Nucleic Acid Atoms
Solvent Atoms294
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data processing
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction