2QTT | pdb_00002qtt

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

X-RAY DIFFRACTION

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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
1.97	37.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.3	α = 90
b = 127.05	β = 109.63
c = 45.45	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 MIRRORS	2005-06-30	M	SINGLE WAVELENGTH
2	1	x-ray		M

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

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
1,2	1.93	23.61	94.8	0.06	12.6	3.17		31340

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)
1,2	1.93	2	90.5		0.155	5.2	2.48

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.93	23.61	28208	3131	94.7	0.17771	0.17158	0.17	0.23275	0.23	RANDOM	19.226

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]
2.58		0.51	-1.2		-1.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.712
r_dihedral_angle_3_deg	13.697
r_dihedral_angle_4_deg	7.623
r_dihedral_angle_1_deg	5.818
r_scangle_it	2.868
r_scbond_it	1.903
r_angle_refined_deg	1.509
r_mcangle_it	1.116
r_mcbond_it	0.636
r_nbtor_refined	0.302
r_nbd_refined	0.228
r_symmetry_vdw_refined	0.183
r_xyhbond_nbd_refined	0.14
r_symmetry_hbond_refined	0.111
r_chiral_restr	0.101
r_bond_refined_d	0.014
r_gen_planes_refined	0.004
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	3687
Nucleic Acid Atoms
Solvent Atoms	440
Heterogen Atoms	33

Software

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