8FER | pdb_00008fer

16mer self-complementary duplex RNA with two continuous s(2)U:s(2)U pairs

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ND4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.02 M Magnesium chloride hexahydrate, 0.002 M Cobalt(II) chloride hexahydrate, 0.05 M HEPES sodium pH 7.5, 2.0 M Ammonium sulfate, 0.001 M Spermine

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.81	α = 90
b = 43.81	β = 90
c = 258.17	γ = 120

Symmetry
Space Group	H 3 2

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 PILATUS3 6M		2022-09-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 2.0.1	1.037690	ALS	2.0.1

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	1.54	50	99.7	0.113	0.121	0.043	0.986	13.7	7.9		14744

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	1.54	1.57	100		0.429	0.461	0.166	0.978	4.4	7.6

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.54	43.065	14221	725	96.101	0.221	0.2187	0.22	0.2587	0.26	14.69

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]
0.002	0.001		0.002		-0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_angle_other_deg	3.873
r_lrange_it	3.249
r_lrange_other	3.248
r_angle_refined_deg	2.757
r_scangle_it	2.216
r_scangle_other	2.215
r_chiral_restr_other	2.028
r_scbond_it	1.593
r_scbond_other	1.592
r_symmetry_nbd_other	0.249
r_nbtor_refined	0.249
r_nbd_other	0.185
r_chiral_restr	0.183
r_nbd_refined	0.151
r_xyhbond_nbd_refined	0.139
r_symmetry_nbtor_other	0.129
r_symmetry_xyhbond_nbd_refined	0.123
r_symmetry_nbd_refined	0.095
r_bond_other_d	0.031
r_gen_planes_refined	0.023
r_bond_refined_d	0.017
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	668
Solvent Atoms	85
Heterogen Atoms

Software

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