6ZW3 | pdb_00006zw3

Racemic compound of RNA duplexes.

X-RAY DIFFRACTION

---

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 polyethylene glycol 8000

Crystal Properties
Matthews coefficient	Solvent content
2	38.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 20.95	α = 106.033
b = 26.49	β = 96.057
c = 38.66	γ = 92.598

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		2018-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	1.283	PETRA III, EMBL c/o DESY	P13 (MX1)

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	1.52	37	86.7	0.168	0.198	0.975	4.19	3.5		10572

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	1.52	1.61			1.061	1.252	0.652

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	1.522	36.874	10553	563	86.756	0.216	0.2128	0.22	0.2721	0.27	20.915

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]
-0.731	0.709	0.242	1.541	0.039	-0.802

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	6.742
r_lrange_other	5.432
r_scangle_it	1.873
r_scangle_other	1.872
r_angle_refined_deg	1.436
r_scbond_it	1.304
r_scbond_other	1.303
r_angle_other_deg	1.182
r_symmetry_xyhbond_nbd_other	0.318
r_symmetry_nbd_other	0.272
r_xyhbond_nbd_refined	0.268
r_nbtor_refined	0.253
r_symmetry_xyhbond_nbd_refined	0.242
r_nbd_refined	0.215
r_nbd_other	0.169
r_symmetry_nbd_refined	0.131
r_metal_ion_refined	0.081
r_chiral_restr	0.062
r_symmetry_nbtor_other	0.062
r_gen_planes_refined	0.015
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	187
Heterogen Atoms	7

Software

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