9CSQ | pdb_00009csq

16mer self-complementary duplex RNA with s(2)C:I 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	6.5	293	0.2 M Calcium acetate hydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 18% w/v Polyethylene glycol 8,000

Crystal Properties
Matthews coefficient	Solvent content
2.2	43.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.405	α = 90
b = 43.405	β = 90
c = 123.136	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 EIGER2 S 9M		2024-06-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.000050	ALS	8.2.1

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	1.54	41.05	99.9	0.052	0.058	0.025	0.998	19	9.4		6923			27.64

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	1.54	1.57	100		0.725	0.805	0.346	0.952	2.5	9.9

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	FREE R-VALUE	1.54	35.952	6881	687	99.279	0.225	0.2221	0.2253	0.2448	0.2457	29.087

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]
-0.005	-0.002		-0.005		0.015

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	5.452
r_lrange_other	5.341
r_scangle_it	4.23
r_scangle_other	4.227
r_scbond_it	3.157
r_scbond_other	3.153
r_angle_refined_deg	2.481
r_angle_other_deg	0.832
r_xyhbond_nbd_refined	0.269
r_dihedral_angle_other_2_deg	0.24
r_nbtor_refined	0.24
r_symmetry_xyhbond_nbd_refined	0.219
r_symmetry_nbd_other	0.211
r_nbd_other	0.15
r_chiral_restr	0.105
r_symmetry_nbd_refined	0.099
r_nbd_refined	0.092
r_symmetry_nbtor_other	0.086
r_gen_planes_refined	0.018
r_bond_refined_d	0.013
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	56
Heterogen Atoms

Software

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