2PT6

The structure of Plasmodium falciparum spermidine synthase in complex with decarboxylated S-adenosylmethionine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2I7C 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.528825% PEG3350, 0.1 M Ammonium Sulphate and 0.1 M Bis-Tris, 2.5 mM dcAdoMet, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K
Crystal Properties
Matthews coefficientSolvent content
2.8957.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 196.3α = 90
b = 134.18β = 94.38
c = 48.32γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2006-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-21.043MAX III911-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
122096.10.720.11513.673.22807802230.07
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0511000.26929.35.253.2238389

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2I7C219.997937241781000.182170.182170.180480.21407RANDOM30.935
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]
1.85-2.02-2.220.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.799
r_dihedral_angle_4_deg17.677
r_dihedral_angle_3_deg14.351
r_dihedral_angle_1_deg6.098
r_scangle_it3.125
r_scbond_it2.006
r_mcangle_it1.358
r_angle_refined_deg1.302
r_mcbond_it0.823
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.799
r_dihedral_angle_4_deg17.677
r_dihedral_angle_3_deg14.351
r_dihedral_angle_1_deg6.098
r_scangle_it3.125
r_scbond_it2.006
r_mcangle_it1.358
r_angle_refined_deg1.302
r_mcbond_it0.823
r_nbtor_refined0.303
r_symmetry_hbond_refined0.266
r_nbd_refined0.205
r_symmetry_vdw_refined0.201
r_xyhbond_nbd_refined0.158
r_chiral_restr0.091
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6753
Nucleic Acid Atoms
Solvent Atoms403
Heterogen Atoms124

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
REFMACrefinement
REFMACrefinement
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing