Experiment: 7Z6O

X-Ray studies of Ku70/80 reveal the binding site for IP6

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JEY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	24% PEG3350, 200mM Na2SO4, 100mM BTP, 5 mM b-mercaptoethanol

Crystal Properties
Matthews coefficient	Solvent content
4.26	71.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.146	α = 90
b = 125.146	β = 90
c = 319.7	γ = 120

Symmetry
Space Group	P 32 2 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 9M		2020-03-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.980101	SOLEIL	PROXIMA 2

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	3.7	48.3	99.7	0.996	4.2	20.1		31855			115.41

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	3.7	3.79	98.4		0.047		18.1

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1jey	3.7	48.3	1.35	12778	655	40.07	0.2205	0.2179	0.23	0.2713	0.2871	RANDOM	209.23

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	15.5248
f_angle_d	0.4224
f_chiral_restr	0.0375
f_plane_restr	0.003
f_bond_d	0.0016

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8326
Nucleic Acid Atoms	571
Solvent Atoms
Heterogen Atoms	36

Software

Software
Software Name	Purpose
BUSTER	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
STARANISO	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
MxCuBE	data collection
Coot	model building