5N5U

Structure of p-boronophenylalanyl tRNA synthetase in complex with p-boronophenylalanine and adenosine monophosphate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	20 % (w/v) PEG 1000, 0.2 M MgCl2, 0.1 M sodium cacodylate

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.582	α = 90
b = 38.735	β = 90.28
c = 82.034	γ = 90

Symmetry
Space Group	P 1 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 225 mm CCD		2016-06-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.3	0.8943	BESSY	14.3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	1.6	30	99.7	0.043	0.046	1	24.36	7.43		43906		-3	31.967

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.7	99.5		0.717	0.771	0.909	3.18	7.497

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	4NDA	1.6	30	41806	2100	99.67	0.1777	0.176	0.2129	RANDOM	33.232

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]
-1.09		-1.16	1.97		-0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.283
r_dihedral_angle_4_deg	16.369
r_dihedral_angle_3_deg	14.23
r_dihedral_angle_1_deg	5.892
r_angle_refined_deg	2.051
r_angle_other_deg	1.055
r_chiral_restr	0.131
r_bond_refined_d	0.021
r_gen_planes_refined	0.011
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.283
r_dihedral_angle_4_deg	16.369
r_dihedral_angle_3_deg	14.23
r_dihedral_angle_1_deg	5.892
r_angle_refined_deg	2.051
r_angle_other_deg	1.055
r_chiral_restr	0.131
r_bond_refined_d	0.021
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2473
Nucleic Acid Atoms
Solvent Atoms	222
Heterogen Atoms	41

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	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 R01GM133198.