5Y3E

Crystal structure of SARS coronavirus papain-like protease in complex with glycerol


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8295PEG8000, HEPES
Crystal Properties
Matthews coefficientSolvent content
2.6453.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 151.179α = 90
b = 33.357β = 124.98
c = 90.89γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2017-03-03MSINGLE 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
11.6574.4795.50.04726.33.543398
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)
11.651.7194.80.4563.63.7

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 REPLACEMENTTHROUGHOUT2fe81.6574.4741221217595.340.163680.161750.19931RANDOM27.336
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]
-1.29-0.370.920.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.523
r_sphericity_free17.131
r_dihedral_angle_3_deg13.101
r_dihedral_angle_4_deg10.299
r_dihedral_angle_1_deg5.633
r_sphericity_bonded5.456
r_long_range_B_refined2.431
r_long_range_B_other2.379
r_scangle_other2.025
r_mcangle_it1.956
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.523
r_sphericity_free17.131
r_dihedral_angle_3_deg13.101
r_dihedral_angle_4_deg10.299
r_dihedral_angle_1_deg5.633
r_sphericity_bonded5.456
r_long_range_B_refined2.431
r_long_range_B_other2.379
r_scangle_other2.025
r_mcangle_it1.956
r_mcangle_other1.956
r_scbond_it1.858
r_scbond_other1.858
r_mcbond_it1.652
r_mcbond_other1.646
r_rigid_bond_restr1.296
r_angle_refined_deg1.257
r_angle_other_deg0.863
r_chiral_restr0.074
r_bond_refined_d0.008
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 Atoms214
Heterogen Atoms24

Software

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