8FEP | pdb_00008fep

16mer self-complementary duplex RNA with two continuous native U: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		293	2 M Lithium sulfate, 3 % w/v 2-Methyl-2,4-pentanediol

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.717	α = 90
b = 41.717	β = 90
c = 126.234	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 EIGER X 16M		2022-04-23	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	1.55	21.05	98.48	0.066	0.07	0.025	0.999	30	8.8		6354

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	1.55	1.58	100		0.187	0.199	0.066	0.994	2.1	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	MOLECULAR REPLACEMENT	THROUGHOUT	1.55	21.048	6353	327	98.42	0.209	0.2059	0.21	0.2692	0.28	25.459

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		0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	4.477
r_lrange_other	4.424
r_scangle_it	2.942
r_scangle_other	2.939
r_angle_refined_deg	2.548
r_scbond_it	2.35
r_scbond_other	2.347
r_angle_other_deg	0.734
r_nbd_other	0.394
r_symmetry_xyhbond_nbd_refined	0.318
r_xyhbond_nbd_refined	0.287
r_nbtor_refined	0.247
r_chiral_restr	0.226
r_symmetry_nbd_refined	0.212
r_symmetry_nbd_other	0.191
r_symmetry_nbtor_other	0.092
r_nbd_refined	0.086
r_gen_planes_refined	0.023
r_bond_refined_d	0.011
r_bond_other_d	0.006
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	334
Solvent Atoms	55
Heterogen Atoms

Software

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