4OUD

Engineered tyrosyl-tRNA synthetase with the nonstandard amino acid L-4,4-biphenylalanine

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2YXN	PDB entry 2YXN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	0.1 M sodium malonate, 18 % PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.34	α = 90
b = 67.205	β = 102.65
c = 90.682	γ = 90

Symmetry
Space Group	P 1 21 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			2013-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.977	ALS	5.0.1

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	2.65	50	99	0.074	29.2	7.6	27201	26929	1	1

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	2.65	2.74	98.4		0.495	4.65	7.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 2YXN	2.65	45	26709	26407	1398	98.87	0.22592	0.2218	0.30634	RANDOM	58.281

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]
-3.61		0.23	2.41		0.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.786
r_dihedral_angle_4_deg	19.721
r_dihedral_angle_3_deg	18.931
r_dihedral_angle_1_deg	8.728
r_long_range_B_refined	6.309
r_long_range_B_other	6.301
r_mcangle_it	4.263
r_mcangle_other	3.962
r_scangle_other	3.849
r_angle_other_deg	3.616
r_mcbond_it	2.544
r_mcbond_other	2.541
r_scbond_it	2.46
r_scbond_other	2.303
r_angle_refined_deg	1.53
r_chiral_restr	0.086
r_bond_refined_d	0.012
r_gen_planes_other	0.008
r_gen_planes_refined	0.006
r_bond_other_d
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	6038
Nucleic Acid Atoms
Solvent Atoms	57
Heterogen Atoms	13

Software

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