7OUO | pdb_00007ouo

Crystal structure of RNA duplex [UCGUGCGA]2 in complex with Ba2+ cation

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		model generated by Coot

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	The crystal of the r(UCGUGCGA)2 duplex was obtained in the presence of its complementary strand UCGCACGA. The crystals grew in the 12th condition of nucleic acid mini-screen from Hampton (10% MPD, 0.040 M Sodium cacodylate trihydrate pH 6.0, 0.012 M Spermine tetrahydrochloride, 0.08M M Potassium chloride, 0.02M M Barium chloride) and further cryoprotected by 35% of MPD.

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.003	α = 90
b = 44.003	β = 90
c = 122.312	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	100	PIXEL	DECTRIS PILATUS 6M		2018-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.000	APS	22-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	2.21	80	99.5	0.04	0.045	1	17.3	5.7		2460

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.21	2.35			1.12	1.24	0.81	1.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	model generated by Coot	2.212	36.383	2459	123	99.434	0.236	0.2337	0.23	0.2857	0.28	70

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]
2.771	1.385		2.771		-8.988

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_other	8.452
r_lrange_it	8.449
r_scangle_it	6.738
r_scangle_other	6.733
r_scbond_it	5.229
r_scbond_other	5.226
r_angle_refined_deg	1.584
r_angle_other_deg	1.401
r_symmetry_nbd_other	0.273
r_nbtor_refined	0.249
r_nbd_other	0.2
r_xyhbond_nbd_refined	0.186
r_nbd_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.169
r_symmetry_xyhbond_nbd_other	0.143
r_symmetry_nbd_refined	0.113
r_chiral_restr	0.087
r_symmetry_nbtor_other	0.075
r_gen_planes_refined	0.024
r_bond_other_d	0.003
r_gen_planes_other	0.001
r_bond_refined_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	336
Solvent Atoms	2
Heterogen Atoms	1

Software

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