2XYV

Crystal structure of the nsp16 nsp10 SARS coronavirus complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FYGPDB ENTRY 2FYG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.567 MM M CHES, 0.99 M MGCL2-HEXAYDRATE, 33 MM TRIS-HCL, 8.3% (V/V) PEG 8000, FROZEN IN THE PRESENCE OF 15% (V/V) GLYCEROL, pH 8.5
Crystal Properties
Matthews coefficientSolvent content
4.1770.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.151α = 90
b = 184.8β = 90
c = 129.015γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210MIRRORS2010-06-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
12.0537.5299.60.117.53.7510332
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)
12.052.161000.353.23.7

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2FYG2.0645.4146336247596.220.202050.20040.23361RANDOM33.944
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]
0.09-0.110.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.006
r_dihedral_angle_4_deg13.929
r_dihedral_angle_3_deg12.795
r_dihedral_angle_1_deg5.024
r_scangle_it1.706
r_scbond_it1.05
r_angle_refined_deg0.965
r_mcangle_it0.892
r_mcbond_it0.478
r_chiral_restr0.063
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.006
r_dihedral_angle_4_deg13.929
r_dihedral_angle_3_deg12.795
r_dihedral_angle_1_deg5.024
r_scangle_it1.706
r_scbond_it1.05
r_angle_refined_deg0.965
r_mcangle_it0.892
r_mcbond_it0.478
r_chiral_restr0.063
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3043
Nucleic Acid Atoms
Solvent Atoms365
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
CCP4data scaling
PHASERphasing