2HTE

The crystal structure of spermidine synthase from p. falciparum in complex with 5'-methylthioadenosine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZDZPDB ENTRY 1ZDZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.529125% w/v PEG3350, 0.1M Ammonium Sulphate, 0.1M Bis-Tris, 4 mM 5'-methylthioadenosine, pH 5.5, VAPOR DIFFUSION, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
3.3162.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 197.061α = 90
b = 134.6β = 94.66
c = 48.336γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2006-07-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
125097.80.10815.83.884688827811128.99
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.03810.8771.483.63421

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1ZDZ233.087984978619413598.460.1920.187820.18550.23122RANDOM28.989
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.526
r_dihedral_angle_4_deg16.514
r_dihedral_angle_3_deg15.498
r_dihedral_angle_1_deg6.347
r_scangle_it3.842
r_scbond_it2.558
r_mcangle_it1.695
r_angle_refined_deg1.628
r_mcbond_it1.058
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.526
r_dihedral_angle_4_deg16.514
r_dihedral_angle_3_deg15.498
r_dihedral_angle_1_deg6.347
r_scangle_it3.842
r_scbond_it2.558
r_mcangle_it1.695
r_angle_refined_deg1.628
r_mcbond_it1.058
r_nbtor_refined0.305
r_nbd_refined0.206
r_symmetry_hbond_refined0.169
r_symmetry_vdw_refined0.152
r_xyhbond_nbd_refined0.141
r_chiral_restr0.121
r_bond_refined_d0.018
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6616
Nucleic Acid Atoms
Solvent Atoms571
Heterogen Atoms106

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing