9UU9 | pdb_00009uu9

Stilbene synthase of Cenchrus americanus in complex with resveratrol

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4YJY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	5 mM resveratrol, 10 %(v/v) PEG 400, 10 %(v/v) Glycerol, 0.7 M sodium citrate tribasic pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
3.68	66.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.345	α = 90
b = 137.422	β = 90
c = 179.102	γ = 90

Symmetry
Space Group	I 2 2 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 EIGER X 16M		2024-06-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL10U2	0.979	SSRF	BL10U2

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	1.31	89.712	100	0.997	11.8	13.1		311348			16.4

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	1.31	1.38	99.6		0.434	1	11.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.4	89.712	253124	12640	99.966	0.162	0.1612	0.1618	0.1791	0.1799	22.604

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]
-0.091			-0.587		0.678

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.011
r_dihedral_angle_3_deg	13.14
r_dihedral_angle_2_deg	9.9
r_lrange_it	6.617
r_lrange_other	6.538
r_dihedral_angle_1_deg	6.431
r_scangle_it	5.562
r_scangle_other	5.562
r_scbond_it	3.719
r_scbond_other	3.718
r_mcangle_it	2.764
r_mcangle_other	2.764
r_angle_refined_deg	2.177
r_mcbond_it	2.023
r_mcbond_other	2.012
r_angle_other_deg	0.696
r_symmetry_nbd_refined	0.448
r_nbd_other	0.244
r_nbd_refined	0.231
r_symmetry_nbd_other	0.204
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.163
r_symmetry_xyhbond_nbd_refined	0.157
r_chiral_restr	0.105
r_symmetry_xyhbond_nbd_other	0.092
r_symmetry_nbtor_other	0.083
r_gen_planes_other	0.018
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6038
Nucleic Acid Atoms
Solvent Atoms	688
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
PHASER	phasing