9OKT | pdb_00009okt

16mer self-complementary duplex RNA with dA:U pair sequence 2

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	5.5	293	0.08 M Sodium chloride, 0.02 M Magnesium chloride hexahydrate, 0.04 M Sodium cacodylate trihydrate pH 5.5, 35% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.002 M Hexammine cobalt(III) chloride

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.006	α = 90
b = 41.006	β = 90
c = 123.438	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	99	PIXEL	DECTRIS PILATUS3 2M		2024-12-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.97741	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	1.32	50	96.9	0.06	0.064	0.021	0.992	30.3	9.4		9461

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	1.32	1.34	88.7		0.511	0.543	0.18	0.902	4	8.6

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	1.32	34.128	9356	438	95.792	0.184	0.1828	0.1897	0.2065	0.2079	11.904

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_lrange_it	5.306
r_lrange_other	4.654
r_angle_refined_deg	2.297
r_scangle_it	1.815
r_scangle_other	1.813
r_scbond_it	1.297
r_scbond_other	1.295
r_angle_other_deg	0.694
r_nbtor_refined	0.255
r_xyhbond_nbd_refined	0.253
r_symmetry_nbd_other	0.203
r_symmetry_xyhbond_nbd_refined	0.155
r_nbd_other	0.143
r_nbd_refined	0.092
r_chiral_restr	0.091
r_symmetry_nbd_refined	0.087
r_symmetry_nbtor_other	0.084
r_metal_ion_refined	0.08
r_dihedral_angle_other_2_deg	0.069
r_gen_planes_refined	0.029
r_bond_refined_d	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	335
Solvent Atoms	109
Heterogen Atoms	3

Software

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