8RPK | pdb_00008rpk

AMP-forming Acetyl-CoA synthetase from Chloroflexota bacterium without bound ligand

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, HANGING DROP	6.5	293	HEPES

Crystal Properties
Matthews coefficient	Solvent content
3.43	64.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 161.352	α = 90
b = 161.352	β = 90
c = 814.182	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	mirror	2023-09-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9763	PETRA III, EMBL c/o DESY	P13 (MX1)

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	2.615	272	81.5	0.119	0.122	0.027	0.999	19.1	2.6		100973		-3

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	2.62	2.82	20.4		1.952	2.002	0.445	0.711	1.7	20

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	2.615	272	100973	5010	81.507	0.166	0.1629	0.17	0.2213	0.22	78.727

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]
-0.376	-0.188		-0.376		1.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.936
r_dihedral_angle_6_deg	14.535
r_dihedral_angle_2_deg	10.832
r_lrange_it	9.127
r_lrange_other	9.127
r_scangle_it	7.903
r_scangle_other	7.903
r_dihedral_angle_1_deg	7.689
r_mcangle_it	6.459
r_mcangle_other	6.459
r_scbond_it	5.503
r_scbond_other	5.502
r_mcbond_it	4.613
r_mcbond_other	4.613
r_angle_refined_deg	1.872
r_angle_other_deg	0.615
r_symmetry_nbd_refined	0.252
r_nbd_refined	0.216
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.188
r_nbd_other	0.178
r_xyhbond_nbd_refined	0.139
r_symmetry_xyhbond_nbd_refined	0.096
r_metal_ion_refined	0.088
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.082
r_symmetry_xyhbond_nbd_other	0.046
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19896
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms	5

Software

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