8ZVH

Crystal structure of AetD in complex with L-phenylalanine

X-RAY DIFFRACTION

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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
2.14	42.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.043	α = 90
b = 65.043	β = 90
c = 116.211	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	Bruker PHOTON III		2022-08-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	LIQUID ANODE	BRUKER METALJET	1.34138

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	1.87	32.54	99.4	0.999	17.8	6.3		39895

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	1.87	1.9			0.831

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	1.87	32.54	37561	2002	99.28	0.19476	0.19165	0.25043	RANDOM	33.003

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]
-0.51			-0.51		1.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.094
r_dihedral_angle_4_deg	17.832
r_dihedral_angle_3_deg	17.06
r_long_range_B_refined	6.578
r_long_range_B_other	6.514
r_dihedral_angle_1_deg	6.452
r_scangle_other	4.944
r_mcangle_it	3.743
r_mcangle_other	3.742
r_scbond_it	3.234
r_scbond_other	3.233
r_mcbond_it	2.648
r_mcbond_other	2.646
r_angle_refined_deg	1.498
r_angle_other_deg	1.34
r_chiral_restr	0.078
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
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	3852
Nucleic Acid Atoms
Solvent Atoms	417
Heterogen Atoms	31

Software

Software
Software Name	Purpose
REFMAC	refinement
SAINT	data scaling
SAINT	data reduction
PHASER	phasing