7KUM

LNA 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, HANGING DROP	4.6	293	0.1 M Sodium acetate trihydrate pH 4.6, 2.0 M Sodium formate, 50 mM Magnesium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.769	α = 90
b = 47.769	β = 90
c = 84.122	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 PILATUS3 6M		2020-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.977408	ALS	5.0.1

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	1.71	50	100	0.052	0.054	0.013	0.994	52.3	18.8		12474

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	1.71	1.74			0.475	0.489	0.115	0.994	6.9	17.5

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	1.714	50	11701	611	93.833	0.206	0.2052	0.2202	15.717

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]
-0.005	-0.003		-0.005		0.018

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	5.342
r_lrange_other	5.103
r_angle_other_deg	3.9
r_angle_refined_deg	3.048
r_scangle_it	2.842
r_scangle_other	2.841
r_scbond_it	2.187
r_scbond_other	2.185
r_chiral_restr_other	1.779
r_xyhbond_nbd_refined	0.305
r_symmetry_nbtor_other	0.292
r_nbtor_refined	0.245
r_symmetry_nbd_other	0.22
r_symmetry_xyhbond_nbd_refined	0.181
r_nbd_other	0.172
r_nbd_refined	0.168
r_chiral_restr	0.135
r_symmetry_nbd_refined	0.08
r_symmetry_xyhbond_nbd_other	0.041
r_bond_other_d	0.032
r_bond_refined_d	0.027
r_gen_planes_refined	0.019
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	378
Solvent Atoms	115
Heterogen Atoms	328

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing