8TAV

FphH, Staphylococcus aureus fluorophosphonate-binding serine hydrolases H, boronic acid-based compound N34 bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8FTP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5289.1513uL 10mg/ml FphH (10mM HEPES pH 7.5, 100mM NaCl) were mixed with 5uL N34 (50mM in DMSO) and incubated at RT for ~1 hour. 0.2ul FphH-N34 were mixed with 0.2ul of reservoir solution. Sitting drop reservoir contained 180mM Calcium acetate hydrate, 100mM Tris pH 7.5, 9% w/v PEG 8000 and 9% w/v PEG 1000. Crystal was frozen in a solution of ~25% Ethylenglycol, 75% reservoir.
Crystal Properties
Matthews coefficientSolvent content
2.2244.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.381α = 90
b = 67.381β = 90
c = 55.473γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2023-06-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.9537Australian SynchrotronMX1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.3947.6599.90.0590.0620.01712313.550414
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)RedundancyNumber Unique Reflections (All)
11.391.4197.91.8071.880.5160.6412.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.3947.651.3450356249499.840.16140.16030.1825
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d8.899
f_angle_d1.113
f_chiral_restr0.076
f_bond_d0.009
f_plane_restr0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1940
Nucleic Acid Atoms
Solvent Atoms227
Heterogen Atoms40

Software

Software
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing