8PU5 | pdb_00008pu5

Crystal structure of the Acyl-CoA dehydrogenase FadE1(PA0506) E441A from Pseudomonas aeruginosa complexed with C16CoA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6KPT
experimental model	PDB	6IJC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	0.1M Bis Tris Propane pH 6.5, 0.2M sodium nitrate, 20% w/v PEG 3350, 10% v/v ethylene glycol, 5mM C16CoA

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.955	α = 90
b = 92.955	β = 90
c = 128.782	γ = 120

Symmetry
Space Group	P 31 1 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 EIGER2 XE 9M		2021-11-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92	Diamond	I04-1

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	1.44	128.78	100	0.194	0.197	0.031	0.999	11.5	38.5		114956			15.1

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	1.44	1.46	100		4.451	4.529	0.834	0.3	0.4	29.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.44	80.63	109044	5767	99.92	0.1861	0.18462	0.1943	0.21378	0.2176	RANDOM	22.81

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]
-0.32	-0.16		-0.32		1.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.731
r_dihedral_angle_4_deg	18.008
r_dihedral_angle_3_deg	13.711
r_dihedral_angle_1_deg	5.931
r_long_range_B_refined	5.706
r_long_range_B_other	5.596
r_scangle_other	4.449
r_scbond_it	3.004
r_scbond_other	3.003
r_mcangle_it	2.289
r_mcangle_other	2.289
r_mcbond_it	1.632
r_mcbond_other	1.631
r_angle_refined_deg	1.629
r_angle_other_deg	1.506
r_chiral_restr	0.087
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
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	4563
Nucleic Acid Atoms
Solvent Atoms	421
Heterogen Atoms	107

Software

Software
Software Name	Purpose
REFMAC	refinement
PHASER	phasing
xia2	data scaling
xia2	data reduction