9OKV | pdb_00009okv

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

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9MDY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	293	0.02 M Calcium chloride dihydrate, 0.1 M Sodium acetate trihydrate pH 4.6, 30% v/v (+/-)-2-Methyl-2,4-pentanediol

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.147	α = 90
b = 41.147	β = 90
c = 124.373	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	1.23	50	96.2	0.04	0.043	0.014	1	52	8.3		11714

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	1.23	1.25	62.3		0.214	0.251	0.127	0.945	5.2	3.4

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	1.233	41.458	11595	586	95.771	0.185	0.1834	0.1902	0.2273	0.2351	12.1

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]
-0.003	-0.002		-0.003		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	5.831
r_lrange_other	4.898
r_angle_refined_deg	2.044
r_scangle_it	1.567
r_scangle_other	1.566
r_scbond_it	1.134
r_scbond_other	1.133
r_angle_other_deg	0.828
r_nbd_refined	0.42
r_xyhbond_nbd_refined	0.295
r_symmetry_nbd_other	0.276
r_nbtor_refined	0.242
r_symmetry_xyhbond_nbd_refined	0.228
r_chiral_restr_other	0.22
r_nbd_other	0.13
r_chiral_restr	0.084
r_symmetry_nbd_refined	0.082
r_symmetry_nbtor_other	0.073
r_dihedral_angle_other_2_deg	0.059
r_gen_planes_refined	0.03
r_bond_other_d	0.025
r_bond_refined_d	0.013
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	335
Solvent Atoms	107
Heterogen Atoms

Software

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