9COM | pdb_00009com

FphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, unbound dimer crystal form 5

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8T87

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289.15	0.3 uL 13.9 mg/mL FphE (10mM HEPES pH 7.6, 100mM NaCl) were mixed with 0.15 uL of reservoir solution. Sitting drop reservoir contained 25 uL of 0.2 M Potassium thiocyanate, 0.1 M TRIS pH 8.5 and 22% w/v Polyethylene glycol monomethyl ether 2,000. Crystal was frozen in a solution of ~25% glycerol, 75% reservoir after ~10s soaking in that solution.

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.399	α = 90
b = 86.797	β = 90
c = 137.764	γ = 90

Symmetry
Space Group	P 2 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 EIGER X 16M		2022-06-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.954	Australian Synchrotron	MX2

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	2.04	48.17	99.2	0.068	0.076	0.034	0.999	11.9	4.9		51434

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	2.04	2.1		95.2	1.436	1.602	0.697	0.522		4.9

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	2.04	43.4	1.33	51365	2429	99.01	0.1991	0.1968	0.1965	0.2477	0.2477

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	6.715
f_angle_d	0.912
f_chiral_restr	0.055
f_bond_d	0.008
f_plane_restr	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6593
Nucleic Acid Atoms
Solvent Atoms	206
Heterogen Atoms	1

Software

Software
Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
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.