8CLM

1.80 A crystal structure of RNA/2'-O-methyl-RNA heteroduplex

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7OW0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	1 mM duplex, 1.4 M Li2SO4, 50 mM sodium cacodylate, 1 mM spermine

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.103	α = 90
b = 49.303	β = 97.149
c = 55.868	γ = 90

Symmetry
Space Group	P 1 21 1

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	RIGAKU HyPix-6000HE		2021-04-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	RIGAKU PhotonJet-S	1.54184

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	1.8	19.011	99.7	0.081	0.094	0.046	0.998	11.7	4.2		15124			8.6

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	1.8	1.84	100		0.636	0.747	0.382	0.817	2.1	3.6

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.8	19.011	15077	723	99.413	0.191	0.188	0.2561	26.582

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]
-1.766		0.125	-0.416		2.085

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	6.353
r_lrange_other	5.963
r_scangle_it	3.569
r_scangle_other	3.522
r_scbond_it	2.429
r_scbond_other	2.399
r_angle_refined_deg	1.952
r_angle_other_deg	0.502
r_nbtor_refined	0.24
r_symmetry_nbd_refined	0.223
r_xyhbond_nbd_refined	0.198
r_symmetry_nbd_other	0.195
r_dihedral_angle_other_2_deg	0.189
r_nbd_other	0.178
r_symmetry_xyhbond_nbd_refined	0.144
r_nbd_refined	0.117
r_symmetry_nbtor_other	0.105
r_chiral_restr	0.09
r_gen_planes_refined	0.015
r_bond_refined_d	0.006
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	1158
Solvent Atoms	316
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
Aimless	data scaling
MOLREP	phasing