4MI4 | pdb_00004mi4

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


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 Tris HCl, 20% Ethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4349.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.633α = 90
b = 135.898β = 90
c = 140.528γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDMIRROR2011-11-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.987856APS21-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
11.8483099.60.0838.85.25913059130-335.3
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)
11.8481.8899.80.336.65.1

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3EG71.84828.95559155591297599.230.151150.149360.160.1840.19RANDOM30.563
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]
0.38-1.080.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.945
r_dihedral_angle_4_deg14.358
r_dihedral_angle_3_deg10.177
r_long_range_B_refined7.796
r_long_range_B_other7.629
r_scangle_other5.729
r_dihedral_angle_1_deg4.267
r_scbond_it4.153
r_scbond_other4.152
r_mcangle_it3.342
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.945
r_dihedral_angle_4_deg14.358
r_dihedral_angle_3_deg10.177
r_long_range_B_refined7.796
r_long_range_B_other7.629
r_scangle_other5.729
r_dihedral_angle_1_deg4.267
r_scbond_it4.153
r_scbond_other4.152
r_mcangle_it3.342
r_mcangle_other3.341
r_mcbond_it2.615
r_mcbond_other2.615
r_angle_refined_deg1.931
r_angle_other_deg0.895
r_chiral_restr0.136
r_bond_refined_d0.019
r_gen_planes_refined0.012
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 Atoms547
Heterogen Atoms42

Software

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