2PT9

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2I7C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	288	25% 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 coefficient	Solvent content
2.88	62.75

Crystal Data

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

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MAR CCD 165 mm	mirrors	2006-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-2	1.043	MAX II	I911-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.2	20	98.8	0.086	9.85	3.45		62364	2	-3	39.247

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.5	98.8		0.346	3.8	3.45	19744

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (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-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2I7C	2.2	19.77	-3	2	60721	59243	3119	93.6	0.2	0.19831	0.19615	0.23883	RANDOM	35.374

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	-3.28		0.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.529
r_dihedral_angle_4_deg	21.646
r_dihedral_angle_3_deg	16.66
r_dihedral_angle_1_deg	6.382
r_scangle_it	3.157
r_scbond_it	1.963
r_angle_refined_deg	1.46
r_mcangle_it	1.339
r_mcbond_it	0.759
r_symmetry_vdw_refined	0.45
r_nbtor_refined	0.31
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.146
r_symmetry_hbond_refined	0.116
r_chiral_restr	0.101
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
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 Atoms	Number
Protein Atoms	6744
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms	153

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data reduction
XSCALE	data scaling
PHASER	phasing