2QTG

Crystal Structure of Arabidopsis thaliana 5'-Methylthioadenosine nucleosidase in complex with 5'-methylthiotubercidin

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	295	NH4I, PEG3350, ethylene glycol, pH 7.5, vapor diffusion, hanging drop, temperature 295K, pH 7.50

Crystal Properties
Matthews coefficient	Solvent content
1.93	36.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.58	α = 90
b = 126.05	β = 109.02
c = 45.54	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	IMAGE PLATE	RIGAKU RAXIS IV	MIRRORS	2004-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.84	32.77	95.5	0.06	16.2	6.36		35711			22.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.84	1.91	97.3		0.299	5.7	6.81

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	1.84	32.77	35709	1790	95.5	0.185	0.185	0.19	RANDOM	22.83

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]
1.76		1.62	-1.07		0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.781
r_dihedral_angle_3_deg	13.569
r_dihedral_angle_4_deg	10.56
r_dihedral_angle_1_deg	10.168
r_scangle_it	3.376
r_angle_refined_deg	2.714
r_scbond_it	2.311
r_mcangle_it	1.415
r_mcbond_it	0.872
r_nbtor_refined	0.302
r_symmetry_vdw_refined	0.261
r_nbd_refined	0.237
r_xyhbond_nbd_refined	0.235
r_symmetry_hbond_refined	0.142
r_chiral_restr	0.115
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
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	3672
Nucleic Acid Atoms
Solvent Atoms	351
Heterogen Atoms	48

Software

Software
Software Name	Purpose
d*TREK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
d*TREK	data reduction