3E7W

Crystal structure of DLTA: Implications for the reaction mechanism of non-ribosomal peptide synthetase (NRPS) adenylation domains

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	298	0.1M sodium citrate, 0.2M ammonium acetate, 20% PEG 4000, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.564	α = 90
b = 94.99	β = 90
c = 132.547	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	180	CCD	MAR CCD 165 mm	mirrors	2004-04-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7A	0.9123	EMBL/DESY, HAMBURG	BW7A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.28	30	96.2	0.061	0.075	13.92	2.89	26455	25439		-3	38.783

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.28	2.4	90.4		0.284	0.35	3.9	2.73	3720

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.28	19.92	26455	25261	1503	96.2	0.205	0.256	RANDOM	41.12

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]
22.36			-7.42		-14.94

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.4
c_angle_deg	1.3
c_improper_angle_d	0.92
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4055
Nucleic Acid Atoms
Solvent Atoms	367
Heterogen Atoms	28

Software

Software
Software Name	Purpose
XSCALE	data scaling
SHELX	phasing
CNS	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHELXD	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 R01GM133198.