6ZPF | pdb_00006zpf

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 polyethylene glycol 8000

Crystal Properties
Matthews coefficient	Solvent content
1.98	38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 20.85	α = 106.107
b = 26.5	β = 96.001
c = 38.57	γ = 92.722

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	1.44	40	87.3	0.052	0.061	0.999	11.04	3.5		12417

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	1.44	1.53	74.2		0.293	0.343	0.963	2.49	3.5

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	1.442	36.776	12410	653	87.505	0.204	0.2011	0.21	0.2497	0.26	17.245

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]
-0.832	0.206	-0.676	1.894	0.141	-0.838

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	4.961
r_lrange_other	4.16
r_scangle_it	1.693
r_scangle_other	1.693
r_angle_refined_deg	1.673
r_scbond_it	1.325
r_scbond_other	1.325
r_angle_other_deg	1.206
r_symmetry_nbd_other	0.267
r_xyhbond_nbd_refined	0.262
r_symmetry_xyhbond_nbd_other	0.25
r_nbtor_refined	0.247
r_metal_ion_refined	0.234
r_nbd_refined	0.216
r_symmetry_xyhbond_nbd_refined	0.196
r_nbd_other	0.17
r_symmetry_nbd_refined	0.146
r_chiral_restr	0.061
r_symmetry_nbtor_other	0.059
r_gen_planes_refined	0.023
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	197
Heterogen Atoms	7

Software

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