9TCG | pdb_00009tcg

Crystal Structure of a prebiotic tRNA acceptor stem mimic

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.

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.007	α = 90
b = 32.007	β = 90
c = 281.333	γ = 120

Symmetry
Space Group	P 65 2 2

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 EIGER2 XE 16M		2023-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.916	Diamond	I04

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	2.5	46.89	100	0.088	0.09	0.02	1	24.8	33.2		3624

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)
	2.5	2.6	100		6.622	6.783	1.462	0.388	0.6	35.8

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	2.52	46.889	3396	158	98.179	0.259	0.2577	0.2585	0.2955	0.3003	RANDOM	83.243

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]
-0.227	-0.113		-0.227		0.735

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	13.083
r_lrange_other	13.081
r_scangle_it	6.846
r_scangle_other	6.842
r_scbond_it	4.442
r_scbond_other	4.442
r_angle_refined_deg	1.265
r_angle_other_deg	0.383
r_dihedral_angle_other_2_deg	0.301
r_nbtor_refined	0.248
r_nbd_other	0.236
r_symmetry_xyhbond_nbd_refined	0.223
r_symmetry_nbd_other	0.216
r_xyhbond_nbd_refined	0.169
r_nbd_refined	0.108
r_symmetry_nbd_refined	0.082
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.056
r_symmetry_xyhbond_nbd_other	0.036
r_gen_planes_refined	0.008
r_bond_refined_d	0.005
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	604
Solvent Atoms
Heterogen Atoms

Software

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