4DJ4 | pdb_00004dj4

X-ray structure of mutant N211D of 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	3SNG	PDB ENTRY 3SNG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291	0.16 M Magnesium chloride 0.08 M TRIS pH 8.5 19% w/v Polyethylene glycol 3,350 3.3% Butane-1,4-diol, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.322	α = 90
b = 113.322	β = 90
c = 138.322	γ = 120

Symmetry
Space Group	H 3

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	2010-10-19	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	2.35	35	97.8	0.098	17.7	5.7		26874		-3.7	46.6

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	2.35	2.41	78.5		0.615	2.3	4.7	1524

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	Rfree throughout	PDB ENTRY 3SNG	2.35	35	26873	26873	1349	97.73	0.18617	0.18617	0.1834	0.19	0.2074	0.19	random	40.612

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]
-2.22	-1.11		-2.22		3.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.056
r_dihedral_angle_4_deg	17.785
r_dihedral_angle_3_deg	16.311
r_dihedral_angle_1_deg	5.877
r_angle_refined_deg	1.464
r_angle_other_deg	0.985
r_chiral_restr	0.083
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.056
r_dihedral_angle_4_deg	17.785
r_dihedral_angle_3_deg	16.311
r_dihedral_angle_1_deg	5.877
r_angle_refined_deg	1.464
r_angle_other_deg	0.985
r_chiral_restr	0.083
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4162
Nucleic Acid Atoms
Solvent Atoms	169
Heterogen Atoms	209

Software

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

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.