9Q0I | pdb_00009q0i

Structure of dsRNA 16mer containing 4'-C-methyladenosine

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	294	10% MPD, 40 mM Sodium cacodylate trihydrate pH 6.0 12 mM Spermine, 80 mM KCl

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.038	α = 90
b = 43.038	β = 90
c = 127.318	γ = 120

Symmetry
Space Group	P 31

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 EIGER2 XE 16M		2024-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-1	0.91943	SSRL	BL12-1

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	1.8	37.3	99.7	0.09	0.094	0.029	0.999	11.5	10.3		24409		-3

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	98.7		1.225	1.32	0.482	0.264	1.6	7.3

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	SAD	FREE R-VALUE	1.801	37.3	24365	1252	99.73	0.214	0.2122	0.2257	0.2459	0.254	39.27

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]
0.694	0.347		0.694		-2.251

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	5.212
r_lrange_other	5.199
r_scangle_it	3.572
r_scangle_other	3.571
r_scbond_other	2.725
r_scbond_it	2.724
r_angle_refined_deg	1.803
r_angle_other_deg	0.524
r_nbtor_refined	0.264
r_symmetry_nbd_other	0.197
r_xyhbond_nbd_refined	0.195
r_nbd_other	0.188
r_symmetry_xyhbond_nbd_refined	0.157
r_nbd_refined	0.135
r_dihedral_angle_other_2_deg	0.134
r_symmetry_nbd_refined	0.091
r_symmetry_nbtor_other	0.09
r_chiral_restr	0.063
r_chiral_restr_other	0.061
r_gen_planes_refined	0.013
r_bond_refined_d	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	2034
Solvent Atoms	101
Heterogen Atoms	14

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PDB_EXTRACT	data extraction
AutoSol	phasing