9OC3 | pdb_00009oc3

Transcription factor DeltaFOSB/JUND bZIP domain in complex with an effector molecule

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7UCD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	Delta-FOSB/JUND bZIP crystals were grown at 293 K with the hanging-drop vapor-diffusion method by mixing 2 to 4 microL of Delta-FOSB/JUND bZIP (8-10 mg/ml in 20 mM HEPES pH 7.0, 250 mM NaCl with 1 mM TCEP with an equal volume of reservoir solution consisting of either 100 mM Tris pH 8.5, 35% (v/v) isopropanol or 100 mM Tris pH 7.0, 40% (v/v) ethanol. Crystals grew within 7 days to a final size of 0.1-0.3 mm. The crystals were soaked in 10-20 mM JFD00458 compound (diluted in reservoir solution from 200 mM stock) for 1 hour and cryo-protected in reservoir solution supplemented with 10-20 mM JFD00458 and then flash-cooled by plunging into liquid nitrogen

Crystal Properties
Matthews coefficient	Solvent content
3.03	59.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.208	α = 90
b = 65.869	β = 90
c = 123.389	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	196	PIXEL	DECTRIS PILATUS3 2M		2023-05-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.9774	ALS	5.0.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.729	61.69	91.5	0.073	0.077	0.022	0.999	16.6	12.2		14265			21.35

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.729	1.977	62.4		0.999	1.08	0.395	0.701		7.3

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	1.73	61.69	1.35	14261	692	67.88	0.2144	0.2108	0.2153	0.288	0.2898	35.33

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	18.7501
f_angle_d	1.1422
f_chiral_restr	0.0471
f_bond_d	0.0119
f_plane_restr	0.0114

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1068
Nucleic Acid Atoms
Solvent Atoms	120
Heterogen Atoms	49

Software

Software
Software Name	Purpose
PHENIX	refinement
AutoProcess	data reduction
STARANISO	data scaling
PHASER	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.