9OL1 | pdb_00009ol1

16mer self-complementary duplex RNA with dI:s(2)C 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	9MDY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.2 M Calcium chloride dihydrate, 0.05 M HEPES sodium pH 7.5, 28% v/v Polyethylene glycol 400, 0.002 M Spermine

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.898	α = 90
b = 40.898	β = 90
c = 124.979	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 EIGER X 16M		2025-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.97933	NSLS-II	17-ID-2

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	1.243	34.077	100	0.128	0.135	0.044	0.997	12.5	17.6		11727

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	1.243	1.265	100		2	2.14	0.754	0.439	2	14.7

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	1.243	34.077	11724	1173	99.957	0.191	0.1864	0.1931	0.229	0.2302	12.619

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	4.617
r_lrange_other	4.035
r_angle_refined_deg	2.079
r_scangle_it	1.802
r_scangle_other	1.801
r_scbond_it	1.256
r_scbond_other	1.254
r_angle_other_deg	0.768
r_xyhbond_nbd_refined	0.294
r_nbtor_refined	0.239
r_symmetry_nbd_other	0.205
r_metal_ion_refined	0.199
r_symmetry_xyhbond_nbd_refined	0.185
r_nbd_other	0.147
r_symmetry_nbd_refined	0.097
r_nbd_refined	0.086
r_chiral_restr	0.076
r_symmetry_nbtor_other	0.075
r_dihedral_angle_other_2_deg	0.05
r_gen_planes_refined	0.029
r_bond_refined_d	0.012
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	334
Solvent Atoms	80
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing