4S0K

Biphenylalanine modified threonyl-tRNA synthetase from Pyrococcus abyssi: 11BIF, 42F, 79V, and 123A mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Y2Q	PDB entry 1y2q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	293	0.1M sodium citrate, 15% PEG 6000, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.43	α = 90
b = 79.15	β = 90
c = 90.74	γ = 90

Symmetry
Space Group	I 2 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	PIXEL	DECTRIS PILATUS 6M		2014-03-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97945	SSRL	BL11-1

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	2.1	50	97.9	0.092	8.7	4		11066

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	2.1	2.21	99.2		0.389	3.1	4.1	1594

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1y2q	2.1	50	10543	523	97.39	0.18766	0.1865	0.21159	RANDOM	34.356

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]
-9.64			-1.93		11.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.632
r_dihedral_angle_3_deg	16.612
r_dihedral_angle_4_deg	13.568
r_dihedral_angle_1_deg	7.032
r_long_range_B_refined	6.589
r_long_range_B_other	6.587
r_scangle_other	4.703
r_scbond_it	2.996
r_scbond_other	2.992
r_mcangle_it	2.762
r_mcangle_other	2.761
r_mcbond_it	2.048
r_mcbond_other	2.041
r_angle_refined_deg	1.768
r_angle_other_deg	0.832
r_chiral_restr	0.106
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1117
Nucleic Acid Atoms
Solvent Atoms	50
Heterogen Atoms	7

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
XDS	data scaling