4R57

Crystal structure of spermidine N-acetyltransferase from Vibrio cholerae in complex with acetyl-CoA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3EG7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2 M Sodium Chloride, 20 % PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.448.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 176.732α = 90
b = 176.732β = 90
c = 67.045γ = 120
Symmetry
Space GroupP 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDBeryllium lenses2013-11-06MSINGLE 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)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
12.07940.699.40.08438.15.4140107140107-3
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)
12.0792.1295.20.582.85

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3EG72.07940.6132888132888718899.420.174170.170640.23957RANDOM36.75
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]
2.392.39-4.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.185
r_dihedral_angle_4_deg17.987
r_dihedral_angle_3_deg17.492
r_dihedral_angle_1_deg7.42
r_long_range_B_refined5.376
r_long_range_B_other5.376
r_scangle_other3.238
r_mcangle_it3.025
r_mcangle_other3.025
r_scbond_it2.178
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.185
r_dihedral_angle_4_deg17.987
r_dihedral_angle_3_deg17.492
r_dihedral_angle_1_deg7.42
r_long_range_B_refined5.376
r_long_range_B_other5.376
r_scangle_other3.238
r_mcangle_it3.025
r_mcangle_other3.025
r_scbond_it2.178
r_scbond_other2.178
r_mcbond_it2.109
r_mcbond_other2.092
r_angle_refined_deg1.755
r_angle_other_deg0.884
r_chiral_restr0.101
r_bond_refined_d0.013
r_gen_planes_refined0.007
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 Atoms17191
Nucleic Acid Atoms
Solvent Atoms278
Heterogen Atoms643

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling