2O5R

Crystal structure of Glutamyl-tRNA synthetase 1 (EC 6.1.1.17) (Glutamate-tRNA ligase 1) (GluRS 1) (TM1351) from Thermotoga maritima at 2.5 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1G59	pdb entry 1G59 Chain A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP	8	277	0.2M CaAcetate, 10.0% PEG-8000, 0.1M Imidazole pH 8.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.53	65.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.953	α = 90
b = 69.953	β = 90
c = 283.945	γ = 120

Symmetry
Space Group	P 31 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	CCD	MARMOSAIC 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2006-08-11	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.94926, 0.97925, 0.97939	APS	23-ID-D

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	2.34	47.351	99.9	0.165	6.6			35284			46.8

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	2.34	2.42	100		0.012	1.6	7.26	3322

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	MAD, MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1G59 Chain A	2.34	47.351	30264	1524	85.96	0.236	0.234	0.268	RANDOM	23.855

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]
-0.18	-0.09		-0.18		0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.887
r_dihedral_angle_4_deg	11.053
r_dihedral_angle_3_deg	10.179
r_dihedral_angle_1_deg	3.06
r_angle_refined_deg	1.427
r_angle_other_deg	1.235
r_scangle_it	0.998
r_scbond_it	0.662
r_mcangle_it	0.528
r_mcbond_it	0.347
r_nbtor_refined	0.146
r_nbd_refined	0.144
r_nbd_other	0.117
r_symmetry_vdw_other	0.111
r_symmetry_vdw_refined	0.104
r_chiral_restr	0.083
r_xyhbond_nbd_refined	0.078
r_nbtor_other	0.067
r_mcbond_other	0.044
r_bond_refined_d	0.013
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3828
Nucleic Acid Atoms
Solvent Atoms	60
Heterogen Atoms	9

Software

Software
Software Name	Purpose
SHELX	phasing
SOLVE	phasing
MOLREP	phasing
RESOLVE	phasing
REFMAC	refinement
XSCALE	data scaling
MolProbity	model building
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing