4MHD

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.1 M NaCl, 30% Ethanol, 0.1M Tris HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4850.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.453α = 90
b = 136.012β = 90
c = 139.831γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDBeryllium lenses2011-11-12MSINGLE 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
12.33098.80.06443.87.23023930239-3
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)
12.32.341000.237.97.4

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 3EG72.3229.332871528715152297.930.198520.195610.25377RANDOM54.973
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]
0.38-0.440.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.774
r_dihedral_angle_4_deg16.546
r_dihedral_angle_3_deg10.92
r_long_range_B_refined6.824
r_long_range_B_other6.816
r_scangle_other5.254
r_scbond_it3.802
r_scbond_other3.801
r_mcangle_it3.787
r_mcangle_other3.786
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.774
r_dihedral_angle_4_deg16.546
r_dihedral_angle_3_deg10.92
r_long_range_B_refined6.824
r_long_range_B_other6.816
r_scangle_other5.254
r_scbond_it3.802
r_scbond_other3.801
r_mcangle_it3.787
r_mcangle_other3.786
r_dihedral_angle_1_deg3.477
r_mcbond_it2.774
r_mcbond_other2.773
r_angle_refined_deg1.921
r_angle_other_deg0.859
r_chiral_restr0.129
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms4322
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms30

Software

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