3BWC

Crystal structure of spermidine synthase from Trypanosoma cruzi in complex with SAM at 2.3 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	277	0.1 M Potassium phosphate, 0.04 M Tris-HCl pH 8.0, 0.06 M Tris-HCl pH 9.0, 34% PEG 4000, 2 mM SAM, 5 mM BME, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.08	α = 90
b = 99.943	β = 106.26
c = 69.991	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	RIGAKU SATURN 944		2007-06-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54000

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	2.3	20	97.2	0.094	0.11	13.5	3.8	25208	25208

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	2.3	2.4	95.2		0.427	0.324	3.7	3.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3BWB	2.3	20	24235	24235	1274	100	0.20593	0.20307	0.25912	RANDOM	29.389

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]
-0.23		-0.09	-1.26		1.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.767
r_dihedral_angle_4_deg	14.593
r_dihedral_angle_3_deg	12.908
r_dihedral_angle_1_deg	4.344
r_scangle_it	1.894
r_mcangle_it	1.318
r_scbond_it	1.283
r_angle_refined_deg	1.269
r_mcbond_it	0.829
r_angle_other_deg	0.784
r_nbd_refined	0.224
r_nbd_other	0.19
r_nbtor_refined	0.177
r_symmetry_vdw_other	0.138
r_symmetry_hbond_refined	0.128
r_mcbond_other	0.114
r_xyhbond_nbd_refined	0.112
r_symmetry_vdw_refined	0.085
r_nbtor_other	0.08
r_chiral_restr	0.052
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	4364
Nucleic Acid Atoms
Solvent Atoms	424
Heterogen Atoms	56

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing