9G7P

Crystal structure of Shewanella putrefaciens PE-like toxin, Spx


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IKQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7294.150.2 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.0, 20 % w/v PEG 6000 (condition C10 of the PACT premier Screen, Molecular Dimensions)
Crystal Properties
Matthews coefficientSolvent content
2.6553.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.196α = 90
b = 121.196β = 90
c = 125.216γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2021-07-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
11.79104.831000.280.2870.0620.9977.521.5193517
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)
11.791.8299.73.6953.7840.8110.3390.421.2

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-VALUE1.861104.83172116847699.6940.1870.1850.18370.22040.220234.028
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]
0.4860.2430.486-1.576
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.939
r_dihedral_angle_4_deg15.838
r_dihedral_angle_3_deg11.536
r_dihedral_angle_1_deg6.731
r_lrange_it5.49
r_lrange_other5.44
r_scangle_it3.686
r_scangle_other3.686
r_mcangle_it2.876
r_mcangle_other2.876
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13905
Nucleic Acid Atoms
Solvent Atoms1241
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing