8TE0 | pdb_00008te0

16mer self-complementary duplex RNA with D: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	3ND4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	10 mM Magnesium chloride hexahydrate, 50 mM HEPES sodium pH 7.0, 4.0 M Lithium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.501	α = 90
b = 42.501	β = 90
c = 129.967	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 6M		2023-06-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 2.0.1	1.033216	ALS	2.0.1

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	1.42	50	96.2	0.065	0.069	0.024	0.983	30	7.1		8586

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	1.42	1.44	64.5		0.268	0.345	0.214	0.9	2.8	2

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	1.42	35.414	8160	379	91.398	0.216	0.2146	0.22	0.2376	0.25	11.558

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		-0.001		0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	5.259
r_lrange_other	5.02
r_angle_refined_deg	2.37
r_scangle_it	2.319
r_scangle_other	2.317
r_scbond_it	1.598
r_scbond_other	1.596
r_angle_other_deg	0.637
r_dihedral_angle_other_2_deg	0.575
r_nbd_refined	0.426
r_xyhbond_nbd_refined	0.301
r_nbtor_refined	0.251
r_symmetry_nbd_other	0.206
r_nbd_other	0.117
r_chiral_restr	0.099
r_symmetry_nbtor_other	0.086
r_symmetry_nbd_refined	0.081
r_symmetry_xyhbond_nbd_refined	0.064
r_gen_planes_refined	0.029
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	337
Solvent Atoms	79
Heterogen Atoms	1

Software

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