4QAJ

Crystal structure of Peptidyl-tRNA hydrolase from Pseudomonas aeruginosa at 1.5 Angstrom resolution

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4JC4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	PEG 4000, 5% isoproponal, 100mM HEPES buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.115	α = 90
b = 64.115	β = 90
c = 155.312	γ = 120

Symmetry
Space Group	P 61 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	77	CCD	MARRESEARCH	Mirror	2013-11-02	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)	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	1.5	29.64	99.8	50.3		31169	31169

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	1.5	1.53	99.7		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-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4JC4	1.5	29.64	29552	1571	99.86	0.18206	0.18004	0.22027	RANDOM	24.75

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]
0.09	0.09		0.09		-0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.959
r_dihedral_angle_4_deg	14.041
r_dihedral_angle_3_deg	13.85
r_long_range_B_refined	6.924
r_long_range_B_other	6.62
r_dihedral_angle_1_deg	5.624
r_scangle_other	4.46
r_angle_other_deg	3.674
r_mcangle_other	3.057
r_mcangle_it	3.047
r_scbond_it	3.023
r_scbond_other	3.017
r_mcbond_it	2.166
r_mcbond_other	2.141
r_angle_refined_deg	1.926
r_chiral_restr	0.127
r_bond_refined_d	0.021
r_gen_planes_other	0.019
r_gen_planes_refined	0.011
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1467
Nucleic Acid Atoms
Solvent Atoms	250
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling