6UDC

Spectroscopic and structural characterization of a genetically encoded direct sensor for protein-ligand interactions

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	500 ul of 0.1 M Bis-Tris, pH 6.5, 25% w/v polyethylene glycol 3350 in the reservoir with 2 ul of reservoir buffer mixed with 2 ul of 10 mg/ml of protein in the drop

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.812	α = 90
b = 98.281	β = 112.26
c = 52.647	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	PIXEL	DECTRIS PILATUS3 6M		2018-08-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	1.000	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.1	49.14	97.1	0.725	8.1	1		26913

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.16	92.6		0.582	1.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.1	49.14	24877	2017	96.73	0.1988	0.1942	0.2561	RANDOM	38.704

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]
0.87		-0.27	-0.15		-0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.12
r_dihedral_angle_4_deg	20.566
r_dihedral_angle_3_deg	16.963
r_dihedral_angle_1_deg	8.322
r_angle_refined_deg	1.919
r_angle_other_deg	1.056
r_chiral_restr	0.107
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.12
r_dihedral_angle_4_deg	20.566
r_dihedral_angle_3_deg	16.963
r_dihedral_angle_1_deg	8.322
r_angle_refined_deg	1.919
r_angle_other_deg	1.056
r_chiral_restr	0.107
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3632
Nucleic Acid Atoms
Solvent Atoms	50
Heterogen Atoms	64

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	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.