4ERX

Crystal structure of the complex of peptidyl-tRNA hydrolase from Pseudomonas aeruginosa with diethylene glycol at 2.5 Angstrom resolution

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	0.1M HEPES pH 8.5, PEG 4000, 5% Isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.73	α = 90
b = 64.73	β = 90
c = 156.407	γ = 120

Symmetry
Space Group	P 61

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	IMAGE PLATE	MARRESEARCH	Mirror	2012-01-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.514

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.5	56	99.9	0.108	11.6			12644			48

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.59	100		2

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4DJJ	2.5	56	12644			0.1845	0.2089	RANDOM	38.5516

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]
0.265	-3.229		0.265		-0.531

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	3.378
c_scbond_it	2.245
c_mcangle_it	2.201
c_mcbond_it	1.329

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2934
Nucleic Acid Atoms
Solvent Atoms	163
Heterogen Atoms	14

Software

Software
Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

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.