5WIF

Crystal structure of spermidine/spermine N-acetyltransferase SpeG from Yersinia pestis


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82930.1 M MIB buffer, 25% (w/v) PEG 1500
Crystal Properties
Matthews coefficientSolvent content
2.9257.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.596α = 90
b = 120.114β = 90
c = 122.752γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-300Beryllium lenses2017-04-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.53099.70.050.930.65.726195
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)
12.52.541000.662.75.9

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 REPLACEMENTTHROUGHOUT5CNP2.53024919127699.230.190870.188410.24189RANDOM73.548
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]
-1.22-45.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.46
r_dihedral_angle_3_deg17.307
r_dihedral_angle_4_deg15.732
r_long_range_B_refined8.482
r_long_range_B_other8.482
r_dihedral_angle_1_deg6.93
r_scangle_other6.486
r_mcangle_it5.629
r_mcangle_other5.629
r_scbond_it4.333
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.46
r_dihedral_angle_3_deg17.307
r_dihedral_angle_4_deg15.732
r_long_range_B_refined8.482
r_long_range_B_other8.482
r_dihedral_angle_1_deg6.93
r_scangle_other6.486
r_mcangle_it5.629
r_mcangle_other5.629
r_scbond_it4.333
r_scbond_other4.332
r_mcbond_it3.865
r_mcbond_other3.86
r_angle_refined_deg1.955
r_angle_other_deg1.102
r_chiral_restr0.123
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4280
Nucleic Acid Atoms
Solvent Atoms40
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PHASERphasing