4DFE | pdb_00004dfe

Crystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase III from Burkholderia xenovorans

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HN9	PDB entry 1HN9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	290	Internal tracking number 228627G11. Crystallant (Wizard III/IV G11): 20% PEG 6000, 0.1 M Hepes pH 7.0, 200 mM NaCl. Protein: BuxeA.00171.c.A1 PW33645 at 35 mg/ml in a buffer consisting of 25 mM HEPES pH 7.0, 300-500 mM NaCl, 2 mM DTT, 0.025% sodium azide, 5% glycerol. Cryoprotection was achieved by supplementing the reservoir solution with 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.99	α = 113.72
b = 67.03	β = 89.98
c = 89.2	γ = 100.25

Symmetry
Space Group	P 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	CCD	ADSC QUANTUM 315		2011-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.9774	ALS	5.0.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.35	50	97.8	0.087	11.9	3.3		49242		-3	36.372

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.41	97.5		0.502	2.5	3.3

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	MR, MR	THROUGHOUT	PDB entry 1HN9	2.35	50	49242	2488	97.98	0.229	0.227	0.23	0.275	0.28	RANDOM	30.633

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]
0.12	-0.43	-1.09	-0.37	1.88	1.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.696
r_dihedral_angle_4_deg	19.836
r_dihedral_angle_3_deg	15.564
r_dihedral_angle_1_deg	7.069
r_angle_refined_deg	1.294
r_angle_other_deg	1.167
r_chiral_restr	0.079
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.696
r_dihedral_angle_4_deg	19.836
r_dihedral_angle_3_deg	15.564
r_dihedral_angle_1_deg	7.069
r_angle_refined_deg	1.294
r_angle_other_deg	1.167
r_chiral_restr	0.079
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.006
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9403
Nucleic Acid Atoms
Solvent Atoms	290
Heterogen Atoms	4

Software

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

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.