9CSP | pdb_00009csp

16mer self-complementary duplex RNA with s(2)C:G 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	3ND4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES sodium pH 7.5, 30% v/v Polyethylene glycol 400

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.217	α = 90
b = 41.217	β = 90
c = 123.468	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		2024-06-27	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	1.6	50	97.5	0.106	0.115	0.044	0.937	14.8	7.7		5469

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	1.6	1.63	82.9		0.254	0.293	0.141	0.967	2.7	3.3

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	1.6	34.291	5162	253	91.785	0.179	0.1756	0.1819	0.2641	0.2646	13.518

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		-0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	7.856
r_lrange_other	7.351
r_angle_refined_deg	2.261
r_scangle_it	1.956
r_scangle_other	1.954
r_scbond_it	1.372
r_scbond_other	1.371
r_angle_other_deg	0.742
r_xyhbond_nbd_refined	0.264
r_nbtor_refined	0.242
r_symmetry_xyhbond_nbd_refined	0.219
r_dihedral_angle_other_2_deg	0.217
r_symmetry_nbd_other	0.2
r_nbd_other	0.155
r_nbd_refined	0.093
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.082
r_symmetry_nbd_refined	0.078
r_gen_planes_refined	0.022
r_bond_refined_d	0.011
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	336
Solvent Atoms	103
Heterogen Atoms	2

Software

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