9HZI | pdb_00009hzi

X-ray Crystallographic Structure of 4-OT (F11) in complex with 2-Hydroxycinnamaldehyde

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7PUO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	Reservoir Volume = 500 microliter Reservoir Composition PEG 2000 (15%) Urea (13 mM) Bis-Tris pH 7.0 (0.1 M) Drop Preparation 2-Hydroxycinnamaldehyde was saturated in 5mM KH2PO4 pH 7.3. 4-OT (F11) was diluted from the storage stock (104.6 mg/mL) to the working stock (16mg/mL) using the above saturated solution. Drop Volume= 1microliter protein solution (protein in 5mM KH2PO4 pH 7.3 (16 mg/ml) + 1microliter precipitant solution Drop Composition PEG 2000 (7.5%) Urea (6.5 mM) Bis-Tris pH 7.0 (0.05 M) Guanidine Hydrochloride (0.08 M)

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.685	α = 90
b = 49.888	β = 97.89
c = 87.022	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	DECTRIS EIGER2 XE CdTe 16M		2024-04-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.976256	PETRA III, EMBL c/o DESY	P14 (MX2)

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	2.267	33.357	87.2	0.996	11.9	4.1		13467			41.13

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	2.267	2.306			0.523

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	2.27	33.357	1.34	13455	636	87.12	0.2209	0.2183	0.2171	0.2748	0.2716	49.44

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	11.9068
f_angle_d	0.4185
f_chiral_restr	0.046
f_plane_restr	0.0035
f_bond_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2813
Nucleic Acid Atoms
Solvent Atoms	63
Heterogen Atoms	51

Software

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