3SNG | pdb_00003sng

X-ray structure of fully glycosylated bifunctional nuclease TBN1 from Solanum lycopersicum (Tomato)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AK0	PDB ID 1AK0 was used as a model for replacement into initial MAD maps.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	291	1.0 M Ammonium sulfate, 0.1 M BIS-TRIS pH 5.5, 1% w/v Polyethylene glycol 3,350, VAPOR DIFFUSION, HANGING DROP, temperature 291 K

Crystal Properties
Matthews coefficient	Solvent content
3.33	63.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.031	α = 90
b = 101.031	β = 90
c = 71.529	γ = 120

Symmetry
Space Group	P 31 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	CCD	MARMOSAIC 225 mm CCD	2 mirrors and a double-crystal monochromator	2010-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

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	2.16	35	100	0.094	26.7	11.3	23089	23089		-3.7	36.2

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	2.16	2.24	100		0.597	4.5	11.1	2280

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	Combination of MAD and Molecular replacement	Rfree throughout	PDB ID 1AK0 was used as a model for replacement into initial MAD maps.	2.16	35	23002	23002	1182	99.63	0.18804	0.18804	0.18041	0.19	0.22343	0.2	random	31.642

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]
0.21	0.1		0.21		-0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.866
r_dihedral_angle_4_deg	16.612
r_dihedral_angle_3_deg	14.843
r_dihedral_angle_1_deg	5.549
r_angle_refined_deg	1.569
r_angle_other_deg	0.972
r_chiral_restr	0.097
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.866
r_dihedral_angle_4_deg	16.612
r_dihedral_angle_3_deg	14.843
r_dihedral_angle_1_deg	5.549
r_angle_refined_deg	1.569
r_angle_other_deg	0.972
r_chiral_restr	0.097
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2150
Nucleic Acid Atoms
Solvent Atoms	140
Heterogen Atoms	151

Software

Software
Software Name	Purpose
MxCuBE	data collection
SHELX	model building
SHELXD	phasing
SHELXE	model building
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	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.