9OKY | pdb_00009oky

16mer self-complementary duplex RNA with dG:s(2)C 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	9CSO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	0.1 M BIS-TRIS pH 5.5, 2.0 M Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.422	α = 90
b = 43.422	β = 90
c = 256.437	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		2024-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	0.97648	ALS	5.0.3

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	1.478	50	93.2	0.07	0.075	0.025	0.989	20.2	8.2		15145

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	1.478	1.51	93.6		0.506	0.562	0.237	0.866	2.7	5

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	1.478	30.326	15039	818	92.377	0.222	0.22	0.225	0.2484	0.2519	12.195

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	4.906
r_lrange_other	4.669
r_scangle_it	2.236
r_scangle_other	2.235
r_angle_refined_deg	2.212
r_scbond_it	1.542
r_scbond_other	1.541
r_angle_other_deg	0.719
r_nbtor_refined	0.251
r_xyhbond_nbd_refined	0.193
r_symmetry_nbd_other	0.185
r_symmetry_xyhbond_nbd_refined	0.185
r_nbd_other	0.18
r_symmetry_nbd_refined	0.16
r_chiral_restr	0.109
r_nbd_refined	0.094
r_symmetry_nbtor_other	0.083
r_dihedral_angle_other_2_deg	0.074
r_gen_planes_refined	0.022
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	670
Solvent Atoms	138
Heterogen Atoms

Software

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