4MJ8

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3EG7PDB entry 3EG7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.1M Tris HCl, 20% Ethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8556.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.999α = 90
b = 135.445β = 90
c = 141.188γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDBeryllium lenses2011-11-02MSINGLE 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
12.043099.60.06249.37.34584245842-341.1
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)
12.042.0996.40.27972180

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 REPLACEMENTTHROUGHOUTPDB entry 3EG72.0429.774351843518232099.020.171410.169310.21087RANDOM46.192
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]
5.53-4.24-1.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.331
r_dihedral_angle_4_deg13.658
r_dihedral_angle_3_deg10.73
r_long_range_B_refined7.567
r_long_range_B_other7.546
r_scangle_other5.613
r_scbond_it4.072
r_scbond_other4.071
r_mcangle_it3.82
r_mcangle_other3.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.331
r_dihedral_angle_4_deg13.658
r_dihedral_angle_3_deg10.73
r_long_range_B_refined7.567
r_long_range_B_other7.546
r_scangle_other5.613
r_scbond_it4.072
r_scbond_other4.071
r_mcangle_it3.82
r_mcangle_other3.82
r_dihedral_angle_1_deg3.439
r_mcbond_it2.988
r_mcbond_other2.988
r_angle_refined_deg1.853
r_angle_other_deg0.867
r_chiral_restr0.122
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms4300
Nucleic Acid Atoms
Solvent Atoms314
Heterogen Atoms74

Software

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