6Y7T | pdb_00006y7t

Engineered conjugation of lysine-specific molecular tweezers with ExoS derived peptidic inhibitor enhance affinity towards target protein 14-3-3 through ditopic binding

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4N7G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	Bis-Tris Propane 0.2M sodium acetate trihydrate 20% PEG1000 10% Glycerol pH 7 Grew at 4 degree Celsius after a few days

Crystal Properties
Matthews coefficient	Solvent content
3.54	65.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 145.151	α = 90
b = 63.119	β = 101.29
c = 167.021	γ = 90

Symmetry
Space Group	I 1 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 PILATUS 6M-F		2018-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.97625	EMBL/DESY, HAMBURG	X11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.5	59.9	99.9	0.129	0.151	0.058	0.996	8.2	6.6		51708			34.12

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.57	98.4		0.803	0.954	0.373	0.796	1.9	6.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4N7G	2.5	59.9	49026	2689	99.75	0.2215	0.21895	0.23	0.26754	0.27	RANDOM	46.368

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]
3.93		-0.11	-0.4		-3.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.382
r_dihedral_angle_4_deg	18.754
r_dihedral_angle_3_deg	16.361
r_long_range_B_refined	6.235
r_long_range_B_other	6.223
r_dihedral_angle_1_deg	6.18
r_scangle_other	3.761
r_mcangle_it	2.97
r_mcangle_other	2.969
r_scbond_it	2.576
r_scbond_other	2.576
r_mcbond_it	1.903
r_mcbond_other	1.902
r_angle_refined_deg	1.702
r_angle_other_deg	1.317
r_chiral_restr	0.076
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7369
Nucleic Acid Atoms
Solvent Atoms	367
Heterogen Atoms	141

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing