7A9R | pdb_00007a9r

Racemic compound of RNA duplexes.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6ZQ9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.2 M zinc acetate, 0.1 M cacodylate buffer, 18% w/v polyehtylene glycol 8000.

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 21.095	α = 104.6
b = 25.955	β = 96.804
c = 38.514	γ = 91.765

Symmetry
Space Group	P 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	DECTRIS PILATUS 6M		2019-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	1.283	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.455	36.9	82.2	0.121	0.171	0.978	4.09	1.87		4734

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.455	2.6	61.4		0.352	0.497	0.836

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	6zq9	2.455	36.7	2519	121	87.739	0.183	0.1779	0.19	0.2837	0.3	29.174

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]
-3.158	0.809	-0.006	5.444	0.232	-2.102

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	6.284
r_lrange_other	5.518
r_scangle_it	3.348
r_scangle_other	3.347
r_scbond_it	2.186
r_scbond_other	2.184
r_angle_refined_deg	1.668
r_angle_other_deg	1.248
r_metal_ion_refined	0.386
r_xyhbond_nbd_refined	0.293
r_symmetry_nbd_other	0.283
r_nbtor_refined	0.253
r_nbd_other	0.225
r_symmetry_xyhbond_nbd_refined	0.181
r_nbd_refined	0.164
r_symmetry_nbd_refined	0.139
r_symmetry_xyhbond_nbd_other	0.122
r_chiral_restr	0.068
r_symmetry_nbtor_other	0.062
r_gen_planes_refined	0.011
r_bond_refined_d	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	676
Solvent Atoms	81
Heterogen Atoms	7

Software

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