8P61 | pdb_00008p61

Crystal structure of O'nyong'nyong virus capsid protease (106-256)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5H23 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.150.1 M sodium cacodylate (pH 6.5), 2.2 M ammonium sulfate and 100 mM ethylenediaminetetraacetic acid disodium salt Crystals were cryoprotected in 25% (v/v) glycerol in the reservoir solution and flash-cooled in liquid nitrogen
Crystal Properties
Matthews coefficientSolvent content
2.5451.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.65α = 90
b = 112.13β = 89.97
c = 67.1γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P111.0332PETRA III, DESYP11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.948.4698.90.9612.51.751622
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.940.1570.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.944.86551597210098.8680.2270.22530.230.2680.2742.13
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]
-3.0360.52-1.6584.694
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.445
r_dihedral_angle_3_deg15.509
r_dihedral_angle_2_deg12.157
r_lrange_it11.721
r_lrange_other11.593
r_scangle_it8.667
r_scangle_other8.427
r_dihedral_angle_1_deg8.186
r_mcangle_other5.987
r_mcangle_it5.986
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.445
r_dihedral_angle_3_deg15.509
r_dihedral_angle_2_deg12.157
r_lrange_it11.721
r_lrange_other11.593
r_scangle_it8.667
r_scangle_other8.427
r_dihedral_angle_1_deg8.186
r_mcangle_other5.987
r_mcangle_it5.986
r_scbond_it5.63
r_scbond_other5.431
r_mcbond_it4.069
r_mcbond_other4.046
r_angle_refined_deg1.588
r_angle_other_deg0.609
r_xyhbond_nbd_refined0.181
r_nbd_refined0.163
r_symmetry_nbd_other0.161
r_nbtor_refined0.161
r_ncsr_local_group_30.15
r_ncsr_local_group_50.149
r_nbd_other0.141
r_ncsr_local_group_20.129
r_ncsr_local_group_40.126
r_ncsr_local_group_60.125
r_symmetry_nbd_refined0.108
r_symmetry_xyhbond_nbd_refined0.093
r_ncsr_local_group_10.08
r_symmetry_nbtor_other0.076
r_chiral_restr0.074
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_symmetry_xyhbond_nbd_other0.007
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4514
Nucleic Acid Atoms
Solvent Atoms262
Heterogen Atoms84

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing