3VJR | pdb_00003vjr

Crystal structure of Peptidyl-tRNA hydrolase from Escherichia coli in complex with the CCA-acceptor-T[PSI]C domain of tRNA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PTH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.2	293	100mM acetate buffer, 20% (w/v) 1,4-butanediol, 30mM glycyl-glycyl-glycine , pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.07	α = 90
b = 55.07	β = 90
c = 413.1	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	100	CCD	MARMOSAIC 225 mm CCD		2008-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.000	SPring-8	BL41XU

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	2.4	50	98.1	0.056	0.059	24.94	10.9	27129	27129

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)
1	2.4	2.54	93.7		0.187	0.2	8.2	8.1	4136

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2PTH	2.4	50	26216	26216	1390	99.82	0.19472	0.19472	0.19251	0.19	0.23657	0.23	RANDOM	47.222

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]
3.14	1.57		3.14		-4.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.94
r_dihedral_angle_4_deg	17.257
r_dihedral_angle_3_deg	16.8
r_dihedral_angle_1_deg	5.403
r_scangle_it	2.025
r_angle_refined_deg	1.366
r_scbond_it	1.3
r_mcangle_it	0.936
r_mcbond_it	0.488
r_chiral_restr	0.077

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.94
r_dihedral_angle_4_deg	17.257
r_dihedral_angle_3_deg	16.8
r_dihedral_angle_1_deg	5.403
r_scangle_it	2.025
r_angle_refined_deg	1.366
r_scbond_it	1.3
r_mcangle_it	0.936
r_mcbond_it	0.488
r_chiral_restr	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2960
Nucleic Acid Atoms	1532
Solvent Atoms	139
Heterogen Atoms

Software

Software
Software Name	Purpose
XDS	data scaling
MOLREP	phasing
REFMAC	refinement
XDS	data reduction

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.