4FOT

Crystal structure of Peptidyl- tRNA Hydrolase from Acinetobacter baumannii at 2.20 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	0.2M HEPES buffer, 25% PEG10000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.55	α = 90
b = 58.46	β = 90
c = 109.25	γ = 90

Symmetry
Space Group	P 21 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	77	CCD	MARRESEARCH	mirror	2012-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97	ESRF	BM14

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	2.2	51.54	99.3	0.1	13		11771	11771

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	2.2	2.32	95		0.311	3.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2PTH	2.2	51.54	11157	11157	552	98.99	0.1834	0.17293	0.17154	0.20066	RANDOM	21.044

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]
-1.11			1.36		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.177
r_dihedral_angle_4_deg	18.537
r_dihedral_angle_3_deg	17.234
r_dihedral_angle_1_deg	6.015
r_scangle_it	5.929
r_scbond_it	3.841
r_mcangle_it	2.351
r_angle_refined_deg	1.934
r_mcbond_it	1.306
r_chiral_restr	0.149

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.177
r_dihedral_angle_4_deg	18.537
r_dihedral_angle_3_deg	17.234
r_dihedral_angle_1_deg	6.015
r_scangle_it	5.929
r_scbond_it	3.841
r_mcangle_it	2.351
r_angle_refined_deg	1.934
r_mcbond_it	1.306
r_chiral_restr	0.149
r_bond_refined_d	0.02
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1476
Nucleic Acid Atoms
Solvent Atoms	135
Heterogen Atoms	17

Software

Software
Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	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 R01GM133198.