4YGO | pdb_00004ygo

Dodecameric structure of spermidine N-acetyltransferase from Vibrio cholerae in intermediate state


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.01 M CaCl2, 0.1 M Tris HCl, 20% Methanol, 25 % MPD
Crystal Properties
Matthews coefficientSolvent content
2.8556.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 155.118α = 90
b = 135.793β = 117.13
c = 72.848γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2011-12-09MSINGLE 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
12.5301000.06525.43.84661054.8
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)
12.52.541000.5923.8

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3EG72.53044197240899.350.183680.180110.180.252740.25RANDOM61.62
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]
-3.99-1.540.63.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.805
r_dihedral_angle_3_deg18.511
r_dihedral_angle_4_deg18.158
r_dihedral_angle_1_deg7.202
r_long_range_B_refined5.587
r_long_range_B_other5.58
r_scangle_other3.846
r_mcangle_it3.069
r_mcangle_other3.069
r_scbond_it2.532
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.805
r_dihedral_angle_3_deg18.511
r_dihedral_angle_4_deg18.158
r_dihedral_angle_1_deg7.202
r_long_range_B_refined5.587
r_long_range_B_other5.58
r_scangle_other3.846
r_mcangle_it3.069
r_mcangle_other3.069
r_scbond_it2.532
r_scbond_other2.532
r_mcbond_it1.979
r_mcbond_other1.978
r_angle_refined_deg1.762
r_angle_other_deg1.052
r_chiral_restr0.104
r_bond_refined_d0.015
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 Atoms8611
Nucleic Acid Atoms
Solvent Atoms144
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
BLU-MAXdata collection
HKL-3000data scaling
PHASERphasing
Cootmodel building
HKL-3000phasing