6ZQ9 | pdb_00006zq9

Racemic compound of RNA duplexes.

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GQ6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.4	293	0.2 M zinc acetate, 0.1 M cacodylate buffer, 18% w/v polyethylene glycol 8000

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 21	α = 105.088
b = 25.93	β = 96.628
c = 38.53	γ = 91.952

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)	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	37	89.4	0.079	0.998	6.88	3.54		11141

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.59	86.3		0.967	0.797	0.89	3.51

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	2GQ6	1.5	36.892	11127	581	89.388	0.195	0.1917	0.2	0.2535	0.26	20.501

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]
-0.906	0.482	-0.118	2.021	-0.228	-0.839

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	4.185
r_lrange_other	3.593
r_scangle_it	1.853
r_scangle_other	1.852
r_angle_refined_deg	1.526
r_scbond_it	1.344
r_scbond_other	1.343
r_angle_other_deg	1.193
r_symmetry_nbd_other	0.277
r_nbtor_refined	0.25
r_symmetry_xyhbond_nbd_refined	0.24
r_xyhbond_nbd_refined	0.223
r_nbd_refined	0.221
r_metal_ion_refined	0.189
r_symmetry_nbd_refined	0.184
r_nbd_other	0.184
r_chiral_restr	0.061
r_symmetry_nbtor_other	0.061
r_symmetry_xyhbond_nbd_other	0.04
r_gen_planes_refined	0.02
r_bond_refined_d	0.008
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	152
Heterogen Atoms	7

Software

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