8QMI

Crystal structure of RNA G2C4 repeats - native model

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	292	0.08 M NaCl, 0.02 M Magnesium chloride hexahydrate, 0.04 M Na cacodylate trihydrate pH 6.0, 35% v/v MPD, 0.012 M Spermine tetrahydrochloride

Crystal Properties
Matthews coefficient	Solvent content
1.68	26.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.759	α = 90
b = 46.637	β = 90
c = 51.492	γ = 90

Symmetry
Space Group	C 2 2 21

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		2020-10-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU PhotonJet-R	1.54056

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.5	21.251	99.9	0.116	0.044	0.124	0.044	0.99	10	7.3		8334

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	1.5	1.58	100		0.553	0.276	0.276	0.846	2.4

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	FREE R-VALUE	1.5	21.251	8309	404	99.628	0.171	0.1682	0.2255	8.629

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]
0.108			0.45		-0.557

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	4.039
r_lrange_other	3.772
r_dihedral_angle_other_2_deg	2.073
r_angle_refined_deg	1.866
r_scangle_it	1.274
r_scangle_other	1.273
r_angle_other_deg	1.195
r_scbond_it	0.835
r_scbond_other	0.835
r_symmetry_xyhbond_nbd_other	0.714
r_symmetry_xyhbond_nbd_refined	0.331
r_xyhbond_nbd_refined	0.273
r_nbtor_refined	0.255
r_symmetry_nbd_other	0.199
r_nbd_refined	0.187
r_nbd_other	0.186
r_symmetry_nbd_refined	0.173
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.073
r_symmetry_metal_ion_refined	0.072
r_metal_ion_refined	0.053
r_gen_planes_refined	0.021
r_gen_planes_other	0.017
r_bond_refined_d	0.007
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	492
Solvent Atoms	108
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
SCALA	data scaling
PHASER	phasing