6UC3 | pdb_00006uc3

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3RY2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	3.5	298	500 ul of 0.1 M Citric Acid, pH 3.5, 3M NaCl in reservoir with 2 ul of reservoir buffer mixed with 2 ul of 10 mg/ml of protein in the drop. Crystals were soaked to pH 5.5 overnight with 3 exchanges

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.209	α = 90
b = 93.11	β = 90
c = 104.369	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	100	PIXEL	DECTRIS PILATUS3 6M	Si(111) and Si(220) double crystal	2019-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.9795	SSRL	BL9-2

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	1.84	69.48	99.2	0.998	16.7	7.1		19561

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	1.84	9.03			0.951

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3RY2	1.84	69.48	18589	969	98.4	0.1759	0.1739	0.18	0.2127	0.22	RANDOM	20.68

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]
0.06			1.88		-1.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.226
r_dihedral_angle_4_deg	20.062
r_dihedral_angle_3_deg	13.325
r_dihedral_angle_1_deg	7.905
r_angle_other_deg	4.015
r_mcangle_it	3.264
r_mcbond_it	2.223
r_mcbond_other	2.219
r_angle_refined_deg	2.051
r_chiral_restr	0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.226
r_dihedral_angle_4_deg	20.062
r_dihedral_angle_3_deg	13.325
r_dihedral_angle_1_deg	7.905
r_angle_other_deg	4.015
r_mcangle_it	3.264
r_mcbond_it	2.223
r_mcbond_other	2.219
r_angle_refined_deg	2.051
r_chiral_restr	0.12
r_bond_refined_d	0.02
r_gen_planes_other	0.018
r_gen_planes_refined	0.01
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1837
Nucleic Acid Atoms
Solvent Atoms	133
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
pointless	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.