9TCA | pdb_00009tca

Crystal Structure of a tRNA acceptor stem mimic at 1.94 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		292	FUSION (Molecular Dimensions Ltd) was used for screening crystallization conditions by the sitting drop vapor diffusion method (Gorrec & Bellini, 2022). Solutions containing the RNA samples (1 mM) in 100 mM HEPES buffer pH 8 and 10 mM MgCl2 were heated at 65 degrees C for 2 minutes, then cooled slowly to room temperature. The RNA solutions were mixed with FUSION solution in a 1:1 ratio for crystallization. The optimized crystallization conditions for the RNAs are listed in Table 1. All crystals grew at 19 degrees C and were cryoprotected in 20% glycerol before flash-cooling in liquid nitrogen.

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 28.82	α = 90
b = 32.38	β = 90
c = 78.45	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	PIXEL	DECTRIS PILATUS 12M		2023-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I23	3.024	Diamond	I23

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	1.94	27.05	97.2	0.058	0.06	0.014	0.972	25.8	23.3		5588

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)
	1.94	1.99	88.5		1.823	2.039	0.872	0.44	1.2	8.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	1.944	27.05	5587	290	96.477	0.248	0.2467	0.249	0.277	0.2857	52.04

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]
0.535			-4.21		3.675

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_other	11.188
r_lrange_it	11.174
r_scangle_it	7.836
r_scangle_other	7.832
r_scbond_it	5.39
r_scbond_other	5.386
r_angle_refined_deg	2.003
r_angle_other_deg	0.584
r_dihedral_angle_other_2_deg	0.31
r_nbtor_refined	0.242
r_xyhbond_nbd_refined	0.172
r_symmetry_nbd_other	0.157
r_nbd_other	0.133
r_nbd_refined	0.121
r_symmetry_nbd_refined	0.121
r_symmetry_xyhbond_nbd_refined	0.096
r_symmetry_nbtor_other	0.071
r_chiral_restr	0.062
r_gen_planes_refined	0.012
r_bond_refined_d	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	602
Solvent Atoms	34
Heterogen Atoms	7

Software

Software
Software Name	Purpose
XDS	data scaling
REFMAC	refinement
Coot	model building
AutoSol	phasing