5UG4

Structure of spermidine N-acetyltransferase SpeG from Vibrio cholerae


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4MI4PDB entry 4MI4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52940.1 M Tris, 50% MPD, 20% ethanol
Crystal Properties
Matthews coefficientSolvent content
2.6854.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.884α = 90
b = 134.635β = 90
c = 137.346γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDberyllium lenses2011-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97857APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.153099.40.0928.514.936218
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)
12.152.298.20.398.3151771

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 REPLACEMENTTHROUGHOUTPDB entry 4MI42.153034406181298.640.170880.169290.19986RANDOM39.589
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]
-0.19-1.261.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.703
r_dihedral_angle_4_deg22.328
r_dihedral_angle_3_deg14.735
r_dihedral_angle_1_deg6.246
r_long_range_B_refined5.942
r_long_range_B_other5.942
r_scangle_other4.307
r_mcangle_it2.943
r_mcangle_other2.942
r_scbond_it2.773
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.703
r_dihedral_angle_4_deg22.328
r_dihedral_angle_3_deg14.735
r_dihedral_angle_1_deg6.246
r_long_range_B_refined5.942
r_long_range_B_other5.942
r_scangle_other4.307
r_mcangle_it2.943
r_mcangle_other2.942
r_scbond_it2.773
r_scbond_other2.773
r_mcbond_it2.013
r_mcbond_other1.976
r_angle_refined_deg1.919
r_angle_other_deg1.079
r_chiral_restr0.119
r_bond_refined_d0.019
r_gen_planes_refined0.01
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 Atoms4313
Nucleic Acid Atoms
Solvent Atoms236
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing