2HDN | pdb_00002hdn

Trypsin-modified Elongation Factor Tu in complex with tetracycline at 2.8 Angstrom resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		an unrefined 2.7 Angstrom model of E. coli trypsin-modified EF-Tu-MgGDP, consisting of residues 9 to 40, 50 to 258 and 260 to 393, plus one Mg ion and GDP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP			Multiple crystals were used to collect the native and each derivative data set. VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
3	58.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.71	α = 90
b = 156.06	β = 95.38
c = 134.83	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	AREA DETECTOR	SDMS			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU

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	2.7	47.3	92.3	0.099				73085

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	an unrefined 2.7 Angstrom model of E. coli trypsin-modified EF-Tu-MgGDP, consisting of residues 9 to 40, 50 to 258 and 260 to 393, plus one Mg ion and GDP	2.8	40	64651	4601	91.6	0.18	0.17	0.223	0.22	random	44.966

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]
6.585		-7.172	-1.468		-5.117

RMS Deviations
Key	Refinement Restraint Deviation
c_mcangle_it	4.366
c_mcbond_it	2.781
c_angle_deg	1.82
c_bond_d	0.02

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16998
Nucleic Acid Atoms
Solvent Atoms	244
Heterogen Atoms	366

Software

Software
Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
MERLOT	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.