8JI3

Crystal structure of AetD in complex with 5,7-dibromo-L-tryptophan and two Fe2+

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.01 M nickel chloride, 20% PEG 2000 MME, 0.1 M Tris, pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.497	α = 90
b = 65.497	β = 90
c = 117.118	γ = 90

Symmetry
Space Group	P 41

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 X 9M		2023-05-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE TPS 05A	0.9998	NSRRC	TPS 05A

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	1.78	25	99.7	0.053	0.061	0.03	0.991	15.7	4.5		47258

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	1.78	1.84	100		0.675	0.758	0.341	0.835		4.8

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.78	23.44	44807	2407	99.54	0.19585	0.19327	0.24361	RANDOM	40.826

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]
-1.12			-1.12		2.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.228
r_dihedral_angle_4_deg	21.179
r_dihedral_angle_3_deg	18.325
r_long_range_B_refined	8.021
r_long_range_B_other	8.021
r_scangle_other	6.376
r_dihedral_angle_1_deg	6.125
r_mcangle_it	4.361
r_mcangle_other	4.36
r_scbond_it	4.219
r_scbond_other	4.218
r_mcbond_it	3.241
r_mcbond_other	3.241
r_angle_refined_deg	1.591
r_angle_other_deg	1.419
r_chiral_restr	0.086
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3793
Nucleic Acid Atoms
Solvent Atoms	200
Heterogen Atoms	39

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing