8RPL

AMP-forming acetyl-CoA synthetase from Chloroflexota bacterium with bound acetyl AMP

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, HANGING DROP	6.5	293	2 uL (protein in 50 mM HEPES pH 7.5, 100 mM KCl) + 2 uL (25% PEG 400, 0.1 M Na-MES, pH 6.5, 0.05 M MnCl2 or MgCl2)

Crystal Properties
Matthews coefficient	Solvent content
4	64.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 161.909	α = 90
b = 161.909	β = 90
c = 817.234	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 EIGER X 16M	Si111	2023-09-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.97630	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (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	2.37	50	99.9	0.142	0.146	0.999	16	20.4		167479		-3	70

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.37	2.56	100		2.9	2.97	0.502	1.13	21.6

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.37	48.304	167354	8378	99.868	0.163	0.1613	0.2007	76.265

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]
0.658	0.329		0.658		-2.134

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.905
r_dihedral_angle_6_deg	14.338
r_dihedral_angle_2_deg	9.946
r_dihedral_angle_other_2_deg	9.47
r_lrange_it	9.01
r_lrange_other	9.01
r_scangle_it	7.511
r_scangle_other	7.511
r_dihedral_angle_1_deg	7.046
r_mcangle_it	5.312
r_mcangle_other	5.312
r_scbond_it	5.092
r_scbond_other	5.091
r_mcbond_it	3.748
r_mcbond_other	3.745
r_angle_refined_deg	1.698
r_angle_other_deg	0.571
r_symmetry_nbd_refined	0.276
r_metal_ion_refined	0.26
r_nbd_refined	0.209
r_nbd_other	0.206
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.136
r_symmetry_xyhbond_nbd_refined	0.089
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.079
r_symmetry_xyhbond_nbd_other	0.055
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19931
Nucleic Acid Atoms
Solvent Atoms	181
Heterogen Atoms	168

Software

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