9U9U | pdb_00009u9u

Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Lys181Lys/Trp185Tyr/His280Ala with (S)-2-fluoro-3-(4-(trifluoromethyl)phenyl)propanoic acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3R3W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	100 mM Tris Ph 8.5,200 mM CaCl2, 20% peg 3350

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.698	α = 90
b = 86.952	β = 109.276
c = 86.02	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	Bruker PHOTON III		2024-08-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	BRUKER D8 VENTURE	1.54

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	2.6	26.65	98.1	0.96	2.5	2.34		70765			21.5061264137

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	2.6	2.63			0.96

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	2.60000346224	26.6499240149	1.33646717113	70765	3875	99.4239550404	0.198747622164	0.195584463986	0.201	0.254217631613	0.2568	21.3441450228

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	13.1238196937
f_angle_d	0.77278145824
f_chiral_restr	0.0292615311159
f_plane_restr	0.00416307694702
f_bond_d	0.00310904683209

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9320
Nucleic Acid Atoms
Solvent Atoms	233
Heterogen Atoms	60

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing
Coot	model building

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.