9OKS | pdb_00009oks

16mer self-complementary duplex RNA with dA:U pair sequence 1

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	0.08 M Sodium chloride, 0.012 M Potassium chloride, 0.02 M Magnesium chloride hexahydrate, 0.04 M Sodium cacodylate trihydrate pH 6.0, 30% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.012 M Spermine tetrahydrochloride

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.204	α = 90
b = 41.204	β = 90
c = 125.586	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		2024-10-30	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	1.5	50	100	0.067	0.071	0.024	0.996	30	8.7		6909

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		0.51	0.544	0.186	0.919	4	8.2

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	41.862	6743	341	97.583	0.168	0.1661	0.1724	0.2099	0.2168	10.313

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]
-0.001			-0.001		0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	5.57
r_lrange_other	5.045
r_angle_refined_deg	2.01
r_scangle_it	1.745
r_scangle_other	1.743
r_scbond_it	1.188
r_scbond_other	1.187
r_angle_other_deg	0.648
r_nbtor_refined	0.25
r_symmetry_nbd_other	0.194
r_xyhbond_nbd_refined	0.189
r_symmetry_xyhbond_nbd_refined	0.163
r_nbd_other	0.124
r_symmetry_nbd_refined	0.109
r_nbd_refined	0.091
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.082
r_dihedral_angle_other_2_deg	0.072
r_metal_ion_refined	0.056
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	88
Heterogen Atoms	2

Software

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