3B7P

Crystal structure of spermidine synthase from Plasmodium falciparum in complex with spermine

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.5	291	25% w/v PEG 3350, 0.1M Ammonium sulfate, 0.1M Bis-tris, pH 5.5, VAPOR DIFFUSION, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.34	63.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 199.483	α = 90
b = 134.584	β = 96.36
c = 48.37	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	IMAGE PLATE	RIGAKU RAXIS IV	Mirrors	2007-05-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	30	98.5	0.068	16.67	3.4	84798	84798			32.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07	90.8		0.472	2.21	3.2	7768

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2PWP	2	29.44	80454	4239	98.83	0.21634	0.21458	0.24978	RANDOM	35.564

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]
0.09		-0.06	-0.05		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.081
r_dihedral_angle_4_deg	22.62
r_dihedral_angle_3_deg	14.082
r_dihedral_angle_1_deg	6.343
r_scangle_it	2.511
r_scbond_it	1.657
r_angle_refined_deg	1.325
r_mcangle_it	1.124
r_mcbond_it	0.662
r_nbtor_refined	0.304
r_nbd_refined	0.196
r_symmetry_vdw_refined	0.16
r_xyhbond_nbd_refined	0.131
r_symmetry_hbond_refined	0.099
r_chiral_restr	0.095
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6753
Nucleic Acid Atoms
Solvent Atoms	574
Heterogen Atoms	102

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASES	phasing