3BWB

Crystal structure of the apo form of spermidine synthase from Trypanosoma cruzi at 2.5 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277	40 % PEG 4000, 6% PEG 20000, 0.1 M Tris-HCl, 0.1 M Potassium phosphate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.05	40

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.669	α = 90
b = 96.996	β = 106.33
c = 69.649	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 315		2005-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.97000	ALS	8.2.2

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	2.5	20	87.5	0.07	0.081	12.23	3.3	16956	16956

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	2.5	2.6	53.6		0.396	0.381	3.2	2.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	SAD	THROUGHOUT	2.5	20	16306	16306	895	89.11	0.20068	0.19796	0.24785	RANDOM	32.099

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]
-1.08		0.19	0.57		0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.519
r_dihedral_angle_3_deg	14.804
r_dihedral_angle_4_deg	14.612
r_dihedral_angle_1_deg	4.954
r_scangle_it	3.41
r_scbond_it	2.293
r_mcangle_it	1.835
r_mcbond_it	1.641
r_angle_refined_deg	1.058
r_angle_other_deg	0.862
r_mcbond_other	0.209
r_symmetry_hbond_refined	0.197
r_symmetry_vdw_other	0.196
r_nbd_refined	0.185
r_nbd_other	0.18
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.133
r_symmetry_vdw_refined	0.109
r_nbtor_other	0.08
r_chiral_restr	0.068
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4500
Nucleic Acid Atoms
Solvent Atoms	100
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
XDS	data reduction
XSCALE	data scaling
SHELXD	phasing