Experiment: 6UGG

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	287	2 uL 20 mg/ml E. coli tRNA(Asp) + 2 uL equilibration solution (50 mM sodium cacodylate, pH 7.5, 30% MPD, 10 mM spermine tetrahydrochloride, 300 mM sodium chloride, 300 mM potassium chloride) + 0.5 uL 0.25% w/v p-coumaric acid, 0.25% w/v phenylurea, 0.25% w/v poly(3-hydroxybutyric acid), 0.25% w/v sulfaguanidine, 0.02 M sodium HEPES, pH 6.8

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.677	α = 90
b = 64.677	β = 90
c = 195.799	γ = 120

Symmetry
Space Group	P 31 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	PIXEL	DECTRIS EIGER X 9M	Monochromator	2017-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.0782	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.95	48.62	94	0.155	0.158	0.029	0.992	15.8	30		35638

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.056	50.8		2.683	2.724	0.468	0.488	1.8	33.7

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 1EHZ	1.95	48.62	30070	1469	88.5	0.2164	0.2154	0.2381	RANDOM	50.999

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]
2.3			2.3		-4.59

RMS Deviations
Key	Refinement Restraint Deviation
r_angle_other_deg	1.298
r_angle_refined_deg	0.85
r_chiral_restr	0.07
r_gen_planes_refined	0.005
r_bond_refined_d	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	3288
Solvent Atoms	23
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
STARANISO	data scaling
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.