8OJ1 | pdb_00008oj1

Crystal structure of the DNA binding domain of M. polymorpha Auxin Response Factor 2 (MpARF2) in complex with High Affinity DNA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6SDG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Required amount of DNA to 2:1 (protein:DNA) stoichiometry was diluted in [20 mM Tris (pH8.0), 500 mM NaCl, 20 mM DTT] and protein was added to final concentration of 5 mg/mL. Crystals of MpARF2-DBD:DNA were obtained in 100 mM Tris pH 7-9, 18-33% PEG2KMME, 18.5% Glycerol by the sitting-drop vapor-diffusion method at 18 deg. C, in drops of 1 uL + 1 uL (protein:reservoir). Crystals appeared in less than a week. Cryo-cooling in liquid nitrogen was carried out using a cryo-protecting solution containing reservoir solution supplemented with 10% glycerol.

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.911	α = 90
b = 80.933	β = 90
c = 146.623	γ = 90

Symmetry
Space Group	I 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2018-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97926	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	2.566	70.86	99.8	0.063	0.066	0.999	20	9.7		15573			78.72

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.566	2.61			1.449	0.715	1.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.57	70.86	1.35	15569	756	99.8	0.2433	0.2424	0.24	0.2592	0.25	84.74

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
f_dihedral_angle_d	23.8244
f_angle_d	0.5389
f_chiral_restr	0.039
f_plane_restr	0.0041
f_bond_d	0.0025

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2235
Nucleic Acid Atoms	448
Solvent Atoms	44
Heterogen Atoms	1

Software

Software
Software Name	Purpose
MxCuBE	data collection
autoPROC	data processing
PHASER	phasing
Coot	model building
PHENIX	refinement

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.