4II9

Crystal structure of Weissella viridescens FemXVv non-ribosomal amino acid transferase in complex with a peptidyl-RNA conjugate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	295	0.1M Tris-sodium citrate buffer, 0.2M ammonium acetate, 33% polyethylene glycol 4k, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.13	α = 90
b = 101.77	β = 102.6
c = 46.32	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	PIXEL	DECTRIS PILATUS 6M	mirrors	2012-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.9791	SOLEIL	PROXIMA 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	1.66	38.12	99.5	0.04	23.8	3.7	44718	44718		-3	23.2

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	1.66	1.76	98.1		0.189	6.9	3.5	7126

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3GKR	1.66	38.12	44718	42482	2236	99.54	0.178	0.17661	0.17487	0.20935	RANDOM	17.328

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]
-0.95		0.41	-1.07		1.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.099
r_dihedral_angle_4_deg	21.742
r_dihedral_angle_3_deg	12.135
r_dihedral_angle_1_deg	5.842
r_angle_refined_deg	2.342
r_chiral_restr	0.17
r_bond_refined_d	0.024
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2727
Nucleic Acid Atoms	68
Solvent Atoms	296
Heterogen Atoms	49

Software

Software
Software Name	Purpose
MX	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

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.