1Y2Q | pdb_00001y2q

Crystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	PEG 8000, Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

Crystal Properties
Matthews coefficient	Solvent content
1.7	27.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.752	α = 90
b = 61.752	β = 90
c = 64.894	γ = 120

Symmetry
Space Group	P 32 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MARRESEARCH	Osmic mirrors	2004-06-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

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	1.95	25	96.7	0.041	25.3	3.3	10459	10459

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)
	1.95	2.02	87.2		0.314	2.25	2.7	928

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	MIR	THROUGHOUT	1.95	25	9957	9957	500	96.91	0.20865	0.20546	0.2	0.27224	0.27	RANDOM	33.317

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]
-0.91	-0.45		-0.91		1.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.178
r_dihedral_angle_4_deg	23.935
r_dihedral_angle_3_deg	16.676
r_dihedral_angle_1_deg	7.088
r_scangle_it	3.162
r_scbond_it	1.911
r_angle_refined_deg	1.324
r_mcangle_it	1.201
r_mcbond_it	0.73
r_nbtor_refined	0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.178
r_dihedral_angle_4_deg	23.935
r_dihedral_angle_3_deg	16.676
r_dihedral_angle_1_deg	7.088
r_scangle_it	3.162
r_scbond_it	1.911
r_angle_refined_deg	1.324
r_mcangle_it	1.201
r_mcbond_it	0.73
r_nbtor_refined	0.3
r_nbd_refined	0.206
r_symmetry_vdw_refined	0.195
r_xyhbond_nbd_refined	0.175
r_symmetry_hbond_refined	0.099
r_chiral_restr	0.089
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1140
Nucleic Acid Atoms
Solvent Atoms	176
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	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.