7YUL

Crystal structure of human BEND6 BEN domain in complex with DNA

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.12 M Ethylene glycol, 0.1 M Sodium HEPES, 0.1 M MOPS (acid), 12.5% MPD (v/v), 12.5% PEG 1000 (v/v), 12.5% PEG3350 (v/v)

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.092	α = 90
b = 39.514	β = 90
c = 43.719	γ = 90

Symmetry
Space Group	P 21 21 2

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	Bruker PHOTON III		2022-05-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	LIQUID ANODE	BRUKER METALJET	1.34138

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.82	27.11	99.4	0.0451	34.15	7.69		11195

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.82	1.85	92.7		0.159	9.77	3.26

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7YUG	1.82	27.11	10599	567	99.37	0.1594	0.1575	0.1943	RANDOM	16.862

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]
-0.04			0.02		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.544
r_dihedral_angle_4_deg	15.154
r_dihedral_angle_3_deg	13.785
r_dihedral_angle_1_deg	6.303
r_angle_refined_deg	1.826
r_angle_other_deg	1.488
r_chiral_restr	0.098
r_gen_planes_refined	0.013
r_bond_refined_d	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	737
Nucleic Acid Atoms	243
Solvent Atoms	140
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
SAINT	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing