Experiment: 7N5V

ZBTB7A Zinc Finger Domain Bound to DNA Duplex Containing GGACCC (Oligo 20)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7N5U	PDB entry 7N5U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	0.1 M Bis-Tris, pH 6.5, 20% PEG5000 MME

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.292	α = 90
b = 60.067	β = 98.502
c = 133.729	γ = 90

Symmetry
Space Group	P 1 21 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 EIGER X 16M		2021-03-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.00000	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	3.08	43.47	96	0.142	0.067	7.8	5.4		27875			88.56

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.08	3.2	86.7		0.531	0.274	0.992	1.8	4.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB entry 7N5U	3.08	43.47	1.33	27642	1391	94.29	0.2627	0.2598	0.2622	0.3136	0.3145	141.4

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	26.2732
f_angle_d	0.5756
f_chiral_restr	0.0347
f_plane_restr	0.004
f_bond_d	0.0035

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1705
Nucleic Acid Atoms	1947
Solvent Atoms	1
Heterogen Atoms	8

Software

Software
Software Name	Purpose
SERGUI	data collection
PHENIX	refinement
SERGUI	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing