5TL7 | pdb_00005tl7

Crystal structure of SARS-CoV papain-like protease in complex with C-terminal domain mouse ISG15


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3E9S3E9S,5JZE
experimental modelPDB 5JZE3E9S,5JZE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829365% (v/v) MPD, 0.1 M Tris [pH 8.0], supplemented with 30% (w/v) Trimethylamine N-oxide dihydrate additive in a 1:5 dilution
Crystal Properties
Matthews coefficientSolvent content
2.2144.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.981α = 90
b = 98.191β = 90
c = 106.636γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002015-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.9786APS21-ID-G

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
12.4472.2399.10.099182.429922
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)
12.442.530.742

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3E9S,5JZE2.4472.2328405152998.880.196150.192110.19440.267440.2578RANDOM64.266
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]
0.09-0.01-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.395
r_dihedral_angle_4_deg21.28
r_dihedral_angle_3_deg15.493
r_dihedral_angle_1_deg6.456
r_long_range_B_refined6.41
r_long_range_B_other6.41
r_scangle_other3.811
r_mcangle_other2.958
r_mcangle_it2.957
r_scbond_it2.476
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.395
r_dihedral_angle_4_deg21.28
r_dihedral_angle_3_deg15.493
r_dihedral_angle_1_deg6.456
r_long_range_B_refined6.41
r_long_range_B_other6.41
r_scangle_other3.811
r_mcangle_other2.958
r_mcangle_it2.957
r_scbond_it2.476
r_scbond_other2.476
r_mcbond_it2.009
r_mcbond_other2.008
r_angle_refined_deg1.434
r_angle_other_deg0.754
r_chiral_restr0.077
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.001
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 Atoms6226
Nucleic Acid Atoms
Solvent Atoms122
Heterogen Atoms2

Software

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