2PSS | pdb_00002pss

The structure of Plasmodium falciparum spermidine synthase in its apo-form

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	5.6	288	23% w/v PEG 3350, 0.1M Ammonium Sulphate, 0.1M Bis-Tris, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 195.63	α = 90
b = 134.18	β = 94.07
c = 48.42	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	MAR scanner 345 mm plate	mirrors	2006-11-28	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	2.2	20	94.3	0.78	0.14	11.59	2.26	134273	59477		-3	37.145

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	2.256	93		0.264	0.351	5.4	2.24	35395

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2I7C	2.2	19.75	2	2	59477	58292	3068	94.3	0.20721	0.20721	0.20511	0.21	0.24728	0.25	RANDOM	37.145

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]
1.73		-3.32	-3.64		1.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.889
r_dihedral_angle_4_deg	22.802
r_dihedral_angle_3_deg	16.131
r_dihedral_angle_1_deg	6.48
r_scangle_it	2.845
r_scbond_it	1.863
r_angle_refined_deg	1.366
r_mcangle_it	1.353
r_mcbond_it	0.776
r_nbtor_refined	0.307
r_nbd_refined	0.205
r_symmetry_vdw_refined	0.159
r_symmetry_hbond_refined	0.158
r_xyhbond_nbd_refined	0.149
r_chiral_restr	0.098
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	6480
Nucleic Acid Atoms
Solvent Atoms	203
Heterogen Atoms	57

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
XDS	data reduction
XSCALE	data scaling
PHASER	phasing