9FTA | pdb_00009fta

Crystal structure of d(GGGGTTTTGGGG) with Zn and K

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3NZ7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		294	30mM NaCaCo(pH6.8), 50mM KCl, 10mM ZnCl2, 2mM Spermine, 5%MPD

Crystal Properties
Matthews coefficient	Solvent content
2	38.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 26.457	α = 89.996
b = 47.925	β = 89.916
c = 96.076	γ = 90.059

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	294	PIXEL	DECTRIS PILATUS 2M		2022-08-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	2	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	2.49	48.04	91.1	0.891	1.11	4		4651			36

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	2.49	2.554			0.891

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.49	48.038	4239	196	91.142	0.338	0.334	0.3376	0.4258	0.4327	35.832

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]
0.116			0.174		-0.291

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	6.406
r_lrange_other	6.396
r_scangle_it	3.154
r_scangle_other	3.153
r_scbond_other	1.979
r_scbond_it	1.978
r_angle_other_deg	1.602
r_angle_refined_deg	1.175
r_nbd_refined	0.377
r_symmetry_nbd_other	0.264
r_nbtor_refined	0.244
r_xyhbond_nbd_refined	0.204
r_metal_ion_refined	0.193
r_nbd_other	0.118
r_symmetry_xyhbond_nbd_other	0.094
r_chiral_restr	0.07
r_symmetry_nbtor_other	0.06
r_symmetry_xyhbond_nbd_refined	0.01
r_gen_planes_refined	0.008
r_symmetry_nbd_refined	0.006
r_bond_refined_d	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	1012
Solvent Atoms	41
Heterogen Atoms	17

Software

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