6TBO

3C-like protease from Southampton virus complexed with FMOPL000363a.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6T1Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.1294Protein concentration 4 mg/ml. 0.2 M ammonium citrate and 12% (v/v) PEG3350.
Crystal Properties
Matthews coefficientSolvent content
2.3146.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.74α = 90
b = 89.46β = 97.45
c = 61.15γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-12-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92819DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.0731.1298.10.1780.2140.1170.9785.13.220052
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.072.1299.20.7160.8590.4680.6151.63.3

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT6t1q2.0731.121905798097.930.20840.20420.2899RANDOM33.8
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]
-2.90.310.222.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.883
r_dihedral_angle_4_deg17.413
r_dihedral_angle_3_deg14.161
r_dihedral_angle_1_deg7.475
r_angle_refined_deg1.598
r_angle_other_deg1.234
r_chiral_restr0.07
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.883
r_dihedral_angle_4_deg17.413
r_dihedral_angle_3_deg14.161
r_dihedral_angle_1_deg7.475
r_angle_refined_deg1.598
r_angle_other_deg1.234
r_chiral_restr0.07
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2577
Nucleic Acid Atoms
Solvent Atoms215
Heterogen Atoms35

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
REFMACphasing