3JXE

Crystal structure of Pyrococcus horikoshii tryptophanyl-tRNA synthetase in complex with TrpAMP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.2	293	0.1M sodium citrate, 1.6M (NH4)2SO4, 10mM MnCl2, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.45	72.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 170.198	α = 90
b = 170.198	β = 90
c = 170.198	γ = 90

Symmetry
Space Group	P 21 3

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	ADSC QUANTUM 270		2008-05-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	1.0000	Photon Factory	BL-17A

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	3	50	100	0.088	33.1	15.5		33131			99.3

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)
	3	3.11	99.5		0.788	2.6	10.3	3255

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3	50	33089	1650	99.9	0.239	0.238	0.258	RANDOM	79.725

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.252
r_dihedral_angle_3_deg	16.929
r_dihedral_angle_4_deg	14.44
r_dihedral_angle_1_deg	4.77
r_angle_refined_deg	0.985
r_scangle_it	0.772
r_scbond_it	0.55
r_mcangle_it	0.547
r_mcbond_it	0.35
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.252
r_dihedral_angle_3_deg	16.929
r_dihedral_angle_4_deg	14.44
r_dihedral_angle_1_deg	4.77
r_angle_refined_deg	0.985
r_scangle_it	0.772
r_scbond_it	0.55
r_mcangle_it	0.547
r_mcbond_it	0.35
r_nbtor_refined	0.303
r_symmetry_vdw_refined	0.228
r_nbd_refined	0.178
r_symmetry_hbond_refined	0.145
r_xyhbond_nbd_refined	0.112
r_chiral_restr	0.071
r_bond_refined_d	0.008
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6035
Nucleic Acid Atoms
Solvent Atoms	12
Heterogen Atoms	84

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.