9SH8 | pdb_00009sh8

Thermus thermophilus asparaginyl-tRNA synthetase with bound sulphamoyl-analogue of asparaginyl-adenylate (AsnAMS)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Native asparaginyl-tRNA synthetase structures

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		288	Native crystals grown with protein 5 mg ml- l, 12-15 % PEG 6000, 0.3M KCI at pH 8.4. Soaked for 15 h in mother liquor containing 100 mM AsnAMS.

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.183	α = 90
b = 125.183	β = 90
c = 126.591	γ = 120

Symmetry
Space Group	P 64 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	100	IMAGE PLATE	MAR scanner 300 mm plate		1997-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.890	ESRF	BM14

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	2.62	14.84	94.5	0.052	9.54	7.1		16965

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	2.62	2.69			0.257

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.62	14.84	16962	1717	93.352	0.215	0.209	0.209	0.2726	0.2726	57.357

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]
-1.168	-0.584		-1.168		3.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.893
r_dihedral_angle_6_deg	10.604
r_lrange_it	6.843
r_dihedral_angle_1_deg	5.941
r_scangle_it	4.006
r_dihedral_angle_2_deg	3.576
r_mcangle_it	3.553
r_scbond_it	2.358
r_mcbond_it	2.09
r_angle_refined_deg	1.061

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.893
r_dihedral_angle_6_deg	10.604
r_lrange_it	6.843
r_dihedral_angle_1_deg	5.941
r_scangle_it	4.006
r_dihedral_angle_2_deg	3.576
r_mcangle_it	3.553
r_scbond_it	2.358
r_mcbond_it	2.09
r_angle_refined_deg	1.061
r_nbtor_refined	0.301
r_nbd_refined	0.185
r_symmetry_nbd_refined	0.116
r_xyhbond_nbd_refined	0.11
r_chiral_restr	0.084
r_symmetry_xyhbond_nbd_refined	0.056
r_gen_planes_refined	0.003
r_bond_refined_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3593
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	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.