7LNG

TNA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5UEE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.1 M HEPES sodium pH 7.5, 1.5 M Lithium sulfate monohydrate

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.165	α = 90
b = 45.165	β = 90
c = 82.831	γ = 120

Symmetry
Space Group	P 3 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	99	PIXEL	DECTRIS EIGER X 16M		2021-02-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.033175	APS	23-ID-B

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	2.2	82.83	99.68	0.103	0.111	0.04	0.996	20	8.9		5325			57.59

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	2.2	2.24	100		0.295	0.312	0.101	0.955	1.3

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5UEE	2.2	82.83	5324	290	99.663	0.228	0.225	0.2747	55.478

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]
-0.556			-0.556		1.112

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	8.328
r_lrange_other	8.324
r_scangle_it	6.744
r_scangle_other	6.742
r_scbond_it	5.028
r_scbond_other	5.025
r_angle_other_deg	4.041
r_angle_refined_deg	2.663
r_chiral_restr_other	1.885
r_symmetry_xyhbond_nbd_refined	0.374
r_nbtor_refined	0.249
r_symmetry_nbd_other	0.229
r_symmetry_nbtor_other	0.228
r_nbd_other	0.211
r_chiral_restr	0.194
r_symmetry_nbd_refined	0.178
r_nbd_refined	0.133
r_xyhbond_nbd_refined	0.117
r_symmetry_xyhbond_nbd_other	0.028
r_bond_other_d	0.025
r_bond_refined_d	0.017
r_gen_planes_refined	0.01
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	378
Solvent Atoms
Heterogen Atoms	318

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
DIALS	data scaling
PHASER	phasing