7OO4 | pdb_00007oo4

HaloTag Engineering for Enhanced Fluorogenicity and Kinetics with a Styrylpyridine Dye

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5Y2X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	293	0.1 M Na3 Cit 5.6 pH 20 %v/v 2-PropOH 20 %w/v PEG 4K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.319	α = 90
b = 68.986	β = 90
c = 86.02	γ = 90

Symmetry
Space Group	P 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 2M-F		2021-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.000031	SLS	X06DA

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	2.1	43.05	99.9	0.1213	0.1265	0.03554	0.999	15.5	12.6		18774

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	2.1	2.175			0.9583	0.9984	0.2778	0.88	2.75

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	5y2x	2.1	43.05	17847	914	99.91	0.2123	0.2097	0.22	0.2632	0.27	RANDOM	37.939

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]
-0.21			-4.49		4.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.084
r_dihedral_angle_4_deg	19.213
r_dihedral_angle_3_deg	16.292
r_dihedral_angle_1_deg	7.273
r_angle_refined_deg	1.673
r_angle_other_deg	1.309
r_chiral_restr	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.084
r_dihedral_angle_4_deg	19.213
r_dihedral_angle_3_deg	16.292
r_dihedral_angle_1_deg	7.273
r_angle_refined_deg	1.673
r_angle_other_deg	1.309
r_chiral_restr	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2342
Nucleic Acid Atoms
Solvent Atoms	37
Heterogen Atoms	29

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	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.