7BHJ | pdb_00007bhj

Crystal structure of 3-hydroxydecanoyl-acyl carrier protein dehydratase (FabA) from Pseudomonas aeruginosa in complex with DDD00084774

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4CL6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	PEG 8000, Magnesium chloride, Tris-HcL

Crystal Properties
Matthews coefficient	Solvent content
3.15	60.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.42	α = 90
b = 142.2	β = 114.68
c = 78.43	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 PILATUS3 6M		2018-10-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.96862	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.11	66.5	99.6	0.064	0.998	10.68	4.05		65125

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.11	2.15			1.298	0.446

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	4CL6	2.11	66.5	61836	3287	99.63	0.204	0.2024	0.21	0.2342	0.24	RANDOM	54.454

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]
2.41		1.21	-0.14		-2.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.686
r_dihedral_angle_4_deg	17.507
r_dihedral_angle_3_deg	15.649
r_dihedral_angle_1_deg	7.732
r_angle_refined_deg	1.57
r_angle_other_deg	1.289
r_chiral_restr	0.07
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.686
r_dihedral_angle_4_deg	17.507
r_dihedral_angle_3_deg	15.649
r_dihedral_angle_1_deg	7.732
r_angle_refined_deg	1.57
r_angle_other_deg	1.289
r_chiral_restr	0.07
r_bond_refined_d	0.009
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	6469
Nucleic Acid Atoms
Solvent Atoms	47
Heterogen Atoms	72

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
DIALS	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.