8BIT

Crystal structure of acyl-CoA synthetase from Metallosphaera sedula in complex with Coenzyme A and acetyl-AMP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.2	293	Protein solution(~3 mg/ml) was mixed to a final volume of 1 uL in 1:1 ratio with reservoir solution containing 0.1M acetate pH 5.2, 0.2M NaCl, 6-8% PEG 1500.

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.806	α = 90
b = 93.19	β = 91.12
c = 131.685	γ = 90

Symmetry
Space Group	C 1 2 1

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 16M		2019-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9763	Diamond	I04

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	3.1	52.95	99.9	0.207	0.246	0.132	0.981	4.2	3.4		23358

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	3.1	3.31		99.9	1.132	1.35	0.728	0.735		3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	3B7W	3.1	52.95	22090	1249	99.79	0.21387	0.21032	0.27664	RANDOM	85.011

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]
3.21		1.21	0.17		-3.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	19.523
r_long_range_B_refined	12.879
r_long_range_B_other	12.879
r_dihedral_angle_2_deg	11.672
r_scangle_other	8.4
r_dihedral_angle_1_deg	7.839
r_mcangle_it	6.924
r_mcangle_other	6.924
r_scbond_it	5.249
r_scbond_other	5.248
r_mcbond_it	4.401
r_mcbond_other	4.4
r_angle_refined_deg	2
r_angle_other_deg	0.645
r_chiral_restr	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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	9039
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	148

Software

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