2PT9

The structure of Plasmodium falciparum spermidine synthase in complex with decarboxylated S-adenosylmethionine and the inhibitor cis-4-methylcyclohexylamine (4MCHA)


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 pH5.5, 2.5 mM dcAdoMet, 2.5 mM 4MCHA, VAPOR DIFFUSION, SITTING DROP, temperature 288K
Crystal Properties
Matthews coefficientSolvent content
2.8862.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 196.24α = 90
b = 134.1β = 94.53
c = 48.35γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2006-12-07MSINGLE 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)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
12.22098.80.0869.853.45623642-339.247
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)
12.22.598.80.3463.83.4519744

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)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 REPLACEMENTTHROUGHOUT2I7C2.219.77-326072159243311993.60.20.198310.196150.23883RANDOM35.374
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]
1.96-2.75-3.280.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.529
r_dihedral_angle_4_deg21.646
r_dihedral_angle_3_deg16.66
r_dihedral_angle_1_deg6.382
r_scangle_it3.157
r_scbond_it1.963
r_angle_refined_deg1.46
r_mcangle_it1.339
r_mcbond_it0.759
r_symmetry_vdw_refined0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.529
r_dihedral_angle_4_deg21.646
r_dihedral_angle_3_deg16.66
r_dihedral_angle_1_deg6.382
r_scangle_it3.157
r_scbond_it1.963
r_angle_refined_deg1.46
r_mcangle_it1.339
r_mcbond_it0.759
r_symmetry_vdw_refined0.45
r_nbtor_refined0.31
r_nbd_refined0.209
r_xyhbond_nbd_refined0.146
r_symmetry_hbond_refined0.116
r_chiral_restr0.101
r_bond_refined_d0.013
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 Atoms6744
Nucleic Acid Atoms
Solvent Atoms173
Heterogen Atoms153

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing