8BIQ | pdb_00008biq

Crystal structure of acyl-COA synthetase from Metallosphaera sedula in complex with acetyl-AMP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.2	293	Drops of 3 mg/ml protein solution dispensed with a Mosquito robot into MRC-SD2 plates containing commercial screens with different ratios (1.25:0.75, 0.75:1.25). Best crystals grown in 0.1M acetic acid pH 5.2, 200mM NaCl, 7-10% PEG3350. Crystals appeared after 24h.

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.864	α = 90
b = 88.289	β = 92.97
c = 131.207	γ = 90

Symmetry
Space Group	P 1 21 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		2019-04-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	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	2.8	66.48	99.7	0.165	0.234	0.165	0.962	3.2	1.9		56843

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	2.8	2.88		99.9	0.817	1.156	0.817	0.527		1.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3B7W	2.8	66.48	54003	2810	99.68	0.23648	0.23456	0.2382	0.27325	0.2469	RANDOM	60.627

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]
1.37		-0.47	-1.28		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.468
r_dihedral_angle_2_deg	14.22
r_dihedral_angle_1_deg	7.708
r_long_range_B_refined	5.865
r_long_range_B_other	5.865
r_scangle_other	2.919
r_mcangle_it	2.457
r_mcangle_other	2.456
r_angle_refined_deg	2.048
r_scbond_it	1.733
r_scbond_other	1.733
r_mcbond_it	1.481
r_mcbond_other	1.481
r_angle_other_deg	0.659
r_chiral_restr	0.087
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
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	18032
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	95

Software

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