6ZR1 | pdb_00006zr1

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 aceate, 0.1 M cacodylate buffer, 18% w/v polyethylene glycol 8000

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 21.13	α = 106.094
b = 26.76	β = 97.185
c = 38.82	γ = 91.419

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 Merge 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	1.528	37	89.2	0.086	0.096	0.997	9.4	5.3		10955

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.528	1.62	74.7		0.557	0.618	0.946	2.03	5.1

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	1.528	36.945	10942	567	89.22	0.205	0.2027	0.21	0.2527	0.25	18.513

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]
0.224	0.384	-0.076	1.073	-0.486	-0.832

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	4.562
r_lrange_other	3.935
r_angle_other_deg	2.37
r_scangle_it	2.047
r_scangle_other	2.046
r_angle_refined_deg	1.737
r_scbond_it	1.561
r_scbond_other	1.56
r_xyhbond_nbd_refined	0.294
r_symmetry_nbd_other	0.271
r_symmetry_xyhbond_nbd_refined	0.255
r_nbtor_refined	0.248
r_nbd_other	0.206
r_nbd_refined	0.205
r_symmetry_xyhbond_nbd_other	0.192
r_metal_ion_refined	0.183
r_symmetry_nbd_refined	0.133
r_symmetry_nbtor_other	0.098
r_chiral_restr	0.091
r_gen_planes_refined	0.02
r_bond_refined_d	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	676
Solvent Atoms	166
Heterogen Atoms	7

Software

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