7OIN

Crystal structure of LSSmScarlet - a genetically encoded red fluorescent protein with a large Stokes shift

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		288	0.1M Lithium sulfate, 0.1M Ammonium acetate, 0.1 M Bis-tris pH 6.5, 23% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.78	30.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.519	α = 90
b = 45.357	β = 102.34
c = 59.042	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	RAYONIX MX-225		2021-04-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	KURCHATOV SNC BEAMLINE K4.4	0.75	KURCHATOV SNC	K4.4

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	1.4	34.43	98	0.137	0.15	0.06	0.991	7.2	6		42242

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	1.4	1.42	100		0.615	0.672	0.268	0.813		6.2

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5LK4	1.4	34.43	40220	2021	97.83	0.1648	0.1635	0.1896	RANDOM	10.778

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]
-0.46		-0.31	-0.09		0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.387
r_dihedral_angle_4_deg	19.478
r_dihedral_angle_3_deg	12.355
r_dihedral_angle_1_deg	7.842
r_angle_refined_deg	2.164
r_angle_other_deg	1.572
r_chiral_restr	0.125
r_bond_refined_d	0.016
r_gen_planes_refined	0.015
r_bond_other_d	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.387
r_dihedral_angle_4_deg	19.478
r_dihedral_angle_3_deg	12.355
r_dihedral_angle_1_deg	7.842
r_angle_refined_deg	2.164
r_angle_other_deg	1.572
r_chiral_restr	0.125
r_bond_refined_d	0.016
r_gen_planes_refined	0.015
r_bond_other_d	0.007
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1778
Nucleic Acid Atoms
Solvent Atoms	272
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
DIALS	data reduction

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 R01GM133198.