2HRA | pdb_00002hra

Crystal structures of the interacting domains from yeast glutamyl-tRNA synthetase and tRNA aminoacylation and nuclear export cofactor Arc1p reveal a novel function for an old fold

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	1.8-1.9 M (NH4)2SO4, 200 mM NaI, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.56	52.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.959	α = 90
b = 107.113	β = 90
c = 167.865	γ = 90

Symmetry
Space Group	C 2 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	100	CCD	MARMOSAIC 225 mm CCD		2004-12-17	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD		2005-04-29	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97925	ESRF	ID23-1
2	SYNCHROTRON	SLS BEAMLINE X06SA	0.97912, 0.97934, 0.95372	SLS	X06SA

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	1.9	80	99.9	0.073	13.2	4.7		37390	-3	-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	1.9	2	99.9		0.36	4.2	4.5	5271

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	MAD	THROUGHOUT	none	1.9	80	-3	35521	35496	1892	99.93	0.21643	0.21643	0.21408	0.23	0.26202	0.28	RANDOM	24.734

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]
3.63			-1.49		-2.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.965
r_dihedral_angle_4_deg	18.84
r_dihedral_angle_3_deg	16.23
r_dihedral_angle_1_deg	6.922
r_scangle_it	3.391
r_scbond_it	2.185
r_angle_refined_deg	1.469
r_mcangle_it	1.348
r_angle_other_deg	0.945
r_mcbond_it	0.8
r_symmetry_metal_ion_refined	0.469
r_symmetry_vdw_refined	0.383
r_symmetry_hbond_refined	0.295
r_symmetry_vdw_other	0.286
r_nbd_refined	0.233
r_mcbond_other	0.201
r_xyhbond_nbd_refined	0.2
r_nbd_other	0.197
r_nbtor_refined	0.183
r_nbtor_other	0.09
r_chiral_restr	0.087
r_metal_ion_refined	0.02
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_xyhbond_nbd_other	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2729
Nucleic Acid Atoms
Solvent Atoms	271
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
SHELXCD	phasing
SHELXD	phasing
SOLVE	phasing
RESOLVE	phasing