8FEQ | pdb_00008feq

16mer self-complementary duplex RNA with two separated 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	6	293	0.075 M Sodium chloride, 0.002 M Calcium chloride dihydrate, 0.05 M Sodium cacodylate trihydrate pH 6.0, 30% w/v 1,6 Hexanediol, 0.0005 M Spermine

Crystal Properties
Matthews coefficient	Solvent content
2	38.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.261	α = 90
b = 41.261	β = 90
c = 124.239	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	1.5	31	100	0.077	0.082	0.029	0.998	14.2	8.7		6853

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	1.5	1.53	100		0.235	0.249	0.081	0.973	2.3	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	1.5	30.993	6848	328	99.883	0.179	0.1774	0.18	0.2103	0.22	18.188

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]
-0.009	-0.004		-0.009		0.028

RMS Deviations
Key	Refinement Restraint Deviation
r_angle_other_deg	3.968
r_lrange_other	3.312
r_lrange_it	3.297
r_angle_refined_deg	2.577
r_chiral_restr_other	2.519
r_scangle_it	2.012
r_scangle_other	2.01
r_scbond_it	1.552
r_scbond_other	1.55
r_nbd_other	0.382
r_nbtor_refined	0.238
r_symmetry_nbd_other	0.207
r_symmetry_nbd_refined	0.202
r_chiral_restr	0.196
r_nbd_refined	0.109
r_symmetry_xyhbond_nbd_refined	0.108
r_xyhbond_nbd_refined	0.103
r_symmetry_nbtor_other	0.092
r_bond_other_d	0.044
r_gen_planes_refined	0.026
r_bond_refined_d	0.021
r_metal_ion_refined	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	54
Heterogen Atoms	1

Software

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