2GT8

Crystal structure of SARS coronavirus main peptidase (with an additional Ala at the N-terminus of each protomer) in the space group P43212


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529850mM ammonium acetate, 6% PEG 8000, 3% ethylene glycol, 1mM dithiothreitol, 0.1M MES (pH 6.5), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.8734.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.294α = 90
b = 70.294β = 90
c = 102.866γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 2102004-08-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.116ALS8.3.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
122599.317964
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0797.8

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 REPLACEMENTTHROUGHOUT2251703491399.370.178210.174870.24092RANDOM23.737
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]
-1.67-1.673.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.37
r_dihedral_angle_4_deg17.666
r_dihedral_angle_3_deg15.848
r_dihedral_angle_1_deg7.118
r_scangle_it4.107
r_scbond_it2.752
r_angle_refined_deg1.765
r_mcangle_it1.755
r_mcbond_it1.052
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.37
r_dihedral_angle_4_deg17.666
r_dihedral_angle_3_deg15.848
r_dihedral_angle_1_deg7.118
r_scangle_it4.107
r_scbond_it2.752
r_angle_refined_deg1.765
r_mcangle_it1.755
r_mcbond_it1.052
r_nbtor_refined0.31
r_symmetry_vdw_refined0.272
r_nbd_refined0.217
r_xyhbond_nbd_refined0.194
r_chiral_restr0.134
r_symmetry_hbond_refined0.098
r_bond_refined_d0.019
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2316
Nucleic Acid Atoms
Solvent Atoms162
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
MOLREPphasing