2PT6 | pdb_00002pt6

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

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, 2.5 mM dcAdoMet, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 196.3	α = 90
b = 134.18	β = 94.38
c = 48.32	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	2006-12-06	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)	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	20	96.1	0.72	0.115	13.67	3.22		80780	2	2	30.07

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)	Redundancy	Number Unique Reflections (All)
1	2	2.051	100		0.269	29.3	5.25	3.22	38389

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 (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2I7C	2	19.99	79372	4178	100	0.18217	0.18217	0.18048	0.19	0.21407	0.22	RANDOM	30.935

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	-2.22		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.799
r_dihedral_angle_4_deg	17.677
r_dihedral_angle_3_deg	14.351
r_dihedral_angle_1_deg	6.098
r_scangle_it	3.125
r_scbond_it	2.006
r_mcangle_it	1.358
r_angle_refined_deg	1.302
r_mcbond_it	0.823
r_nbtor_refined	0.303
r_symmetry_hbond_refined	0.266
r_nbd_refined	0.205
r_symmetry_vdw_refined	0.201
r_xyhbond_nbd_refined	0.158
r_chiral_restr	0.091
r_bond_refined_d	0.012
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	6753
Nucleic Acid Atoms
Solvent Atoms	403
Heterogen Atoms	124

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
REFMAC	refinement
REFMAC	refinement
MAR345dtb	data collection
XDS	data reduction
XSCALE	data scaling
PHASER	phasing