Experiment: 6ONN

Crystal structure of 8-amino-7-oxononanoate synthase from Burkholderia phymatum

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5JAY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	SEC purified BuphA.00096.a.B1.PW38412 at 8.864mg/ml (in 25 mM HEPES pH 7.0, 500 mM NaCl, 5% Glycerol , 2 mM DTT, 0.025% Azide ) was crystallized by sitting drop vapor diffusion at 14C with an equal volume of protein:mother liquor (Morpheus E3: 0.03M Diethylene glycol, 0.03M Triethylene glycol, 0.03M Tetraethylene glycol, 0.03M Pentaethylene glycol, 0.1M Imidazole/MES buffer pH 6.5, 20% Glycerol, 10% PEG4000), then flash-frozen for data collection. Crystal ID 299435e3 data set aas7-2

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.7	α = 90
b = 92.58	β = 90
c = 125.56	γ = 90

Symmetry
Space Group	P 21 21 21

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	RAYONIX MX-300		2018-06-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.8	39.9	99.2	0.068	0.075	0.998	15.99	5.345		84896			29.193

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.85	99.8		0.565	0.624	0.84	3.06	5.371

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5JAY	1.8	39.9	81917	4934	95.7	0.1659	0.1642	0.1647	0.1936	0.1942	28.1894

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5706
Nucleic Acid Atoms
Solvent Atoms	713
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing