2HTE | pdb_00002hte

The crystal structure of spermidine synthase from p. falciparum in complex with 5'-methylthioadenosine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZDZ	PDB ENTRY 1ZDZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.5	291	25% w/v PEG3350, 0.1M Ammonium Sulphate, 0.1M Bis-Tris, 4 mM 5'-methylthioadenosine, pH 5.5, VAPOR DIFFUSION, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.31	62.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 197.061	α = 90
b = 134.6	β = 94.66
c = 48.336	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		2006-07-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	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	50	97.8	0.108	15.8	3.8	84688	82781	1	1	28.99

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	2.03	81		0.877	1.48	3.6	3421

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 (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	PDB ENTRY 1ZDZ	2	33.08	79849	78619	4135	98.46	0.192	0.18782	0.1855	0.18	0.23122	0.23	RANDOM	28.989

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.526
r_dihedral_angle_4_deg	16.514
r_dihedral_angle_3_deg	15.498
r_dihedral_angle_1_deg	6.347
r_scangle_it	3.842
r_scbond_it	2.558
r_mcangle_it	1.695
r_angle_refined_deg	1.628
r_mcbond_it	1.058
r_nbtor_refined	0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.526
r_dihedral_angle_4_deg	16.514
r_dihedral_angle_3_deg	15.498
r_dihedral_angle_1_deg	6.347
r_scangle_it	3.842
r_scbond_it	2.558
r_mcangle_it	1.695
r_angle_refined_deg	1.628
r_mcbond_it	1.058
r_nbtor_refined	0.305
r_nbd_refined	0.206
r_symmetry_hbond_refined	0.169
r_symmetry_vdw_refined	0.152
r_xyhbond_nbd_refined	0.141
r_chiral_restr	0.121
r_bond_refined_d	0.018
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6616
Nucleic Acid Atoms
Solvent Atoms	571
Heterogen Atoms	106

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.