6T6W

3C-like protease from Southampton virus complexed with XST00000692b.


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
2.3547.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.94α = 90
b = 89.46β = 96.89
c = 61.2γ = 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
11.844.7398.60.0980.1170.0630.9948.93.330724
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)
11.81.8599.40.6680.7930.4240.6471.83.4

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 SYNTHESISTHROUGHOUT6t1q1.844.7329227149698.540.1490.1440.2442RANDOM25.94
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]
0.27-0.220.12-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.352
r_dihedral_angle_4_deg20.24
r_dihedral_angle_3_deg15.488
r_dihedral_angle_1_deg7.82
r_rigid_bond_restr2.73
r_angle_refined_deg1.801
r_angle_other_deg1.336
r_chiral_restr0.083
r_bond_refined_d0.011
r_gen_planes_refined0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.352
r_dihedral_angle_4_deg20.24
r_dihedral_angle_3_deg15.488
r_dihedral_angle_1_deg7.82
r_rigid_bond_restr2.73
r_angle_refined_deg1.801
r_angle_other_deg1.336
r_chiral_restr0.083
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2547
Nucleic Acid Atoms
Solvent Atoms314
Heterogen Atoms35

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction
REFMACphasing