8ASK | pdb_00008ask

Crystal structure of d(GCCCACCACGGC)

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		X3DNA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		294	20%MPD, 120mMMgCl2, 60mM NaCaCo, 2mM Spermine

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.49	α = 90
b = 64.49	β = 90
c = 46.19	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	270	PIXEL	DECTRIS PILATUS 2M		2022-08-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	2.00	ELETTRA	5.2R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.95	35.59	96.95	0.992	2	9.2		2783

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.97	3.02			0.3

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	NONE	X3DNA	2.955	35.59	1461	62	96.948	0.129	0.125	0.13	0.2298	0.24	88.593

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]
-0.113	-0.057		-0.113		0.368

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	8.351
r_lrange_other	8.351
r_scangle_it	6.768
r_scangle_other	6.756
r_scbond_it	4.636
r_scbond_other	4.607
r_angle_other_deg	1.751
r_angle_refined_deg	1.196
r_symmetry_nbd_refined	0.343
r_nbd_other	0.301
r_symmetry_nbd_other	0.265
r_nbtor_refined	0.256
r_nbd_refined	0.13
r_xyhbond_nbd_refined	0.122
r_symmetry_xyhbond_nbd_other	0.116
r_symmetry_nbtor_other	0.07
r_chiral_restr	0.069
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	492
Solvent Atoms
Heterogen Atoms

Software

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