9CSR | pdb_00009csr

16mer self-complementary duplex RNA with s(2)C:I 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		293	2.0 M Ammonium sulfate, 5% v/v 2-Propanol

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.942	α = 90
b = 40.942	β = 90
c = 123.477	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		2024-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.000026	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	1.33	50	98.4	0.068	0.072	0.026	0.978	21.6	7.8		9369			13.46

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	1.33	1.35	92		0.471	0.546	0.267	0.85	2.5	3.7

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	FREE R-VALUE	1.33	30.747	9192	451	96.504	0.19	0.188	0.1929	0.2185	0.2223	12.883

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

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	5.286
r_lrange_other	5.148
r_angle_refined_deg	2.348
r_scangle_it	1.937
r_scangle_other	1.935
r_scbond_it	1.396
r_scbond_other	1.395
r_angle_other_deg	0.901
r_xyhbond_nbd_refined	0.241
r_nbtor_refined	0.24
r_symmetry_nbd_other	0.206
r_nbd_other	0.155
r_symmetry_xyhbond_nbd_refined	0.145
r_symmetry_nbd_refined	0.109
r_chiral_restr	0.096
r_nbd_refined	0.088
r_dihedral_angle_other_2_deg	0.08
r_symmetry_nbtor_other	0.08
r_gen_planes_refined	0.029
r_bond_refined_d	0.017
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	84
Heterogen Atoms

Software

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