9WW2 | pdb_00009ww2

Structure of Y50F mutant of fungal flavonoid dehydratase CfvK obtained after 30-minute soak in the substrate solution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	0.1 M sodium citrate tribasic dihydrate (pH 5.0), 1.0 M lithium sulfate, 0.5 M ammonium sulfate and 2% DMSO. Soaked in a solution containing 2 mM 15a-i-15a-v, 0.1 M sodium citrate tribasic dihydrate (pH 5.0), 1.0 M lithium sulfate, 0.5 M ammonium sulfate, and 18 % glycerol for 30 minutes.

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.874	α = 90
b = 91.874	β = 90
c = 108.685	γ = 120

Symmetry
Space Group	H 3 2

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 EIGER2 XE 16M		2025-05-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	1.538	45.94	99.92	0.179	1	16.19	20.3		26366			19.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.54	1.6	99.48		2.714	0.601	1.23	18.9

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	FOURIER SYNTHESIS	FREE R-VALUE	1.54	45.94	1.35	26362	1319	99.92	0.192	0.1905	0.1946	0.2206	0.2243

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	17.5191
f_angle_d	0.854
f_chiral_restr	0.0589
f_plane_restr	0.0088
f_bond_d	0.0057

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1350
Nucleic Acid Atoms
Solvent Atoms	75
Heterogen Atoms	57

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing