9RL6 | pdb_00009rl6

Structure Guided Optimisation of Niclosamide Derivatives as Direct STAT3 Inhibitors Targeting a Novel Binding Site

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4E68

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	278	8% Ethylene Glycol, 0.1M HEPES, 10% PEG8000

Crystal Properties
Matthews coefficient	Solvent content
3.79	67.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 174.263	α = 90
b = 174.263	β = 90
c = 78.762	γ = 90

Symmetry
Space Group	I 41

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 PILATUS3 6M		2018-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	1.00667	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.38	123.3	100	0.081	1	12.2	8		47560

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.38	2.42	99.2		2.91	0.4		8.2

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.55	123.223	37303	1847	96.462	0.217	0.2155	0.2189	0.2494	0.2479	0	87.41

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]
0.354			0.354		-0.708

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	19.964
r_lrange_other	19.751
r_lrange_it	19.737
r_dihedral_angle_2_deg	15.634
r_dihedral_angle_6_deg	14.821
r_mcangle_it	13.849
r_mcangle_other	13.848
r_scangle_it	13.754
r_scangle_other	13.674
r_mcbond_it	9.347
r_mcbond_other	9.346
r_scbond_it	8.945
r_scbond_other	8.944
r_dihedral_angle_1_deg	8.489
r_angle_refined_deg	1.508
r_dihedral_angle_other_2_deg	0.943
r_angle_other_deg	0.82
r_nbd_other	0.357
r_symmetry_nbd_refined	0.348
r_symmetry_xyhbond_nbd_refined	0.283
r_nbd_refined	0.253
r_symmetry_nbd_other	0.24
r_xyhbond_nbd_refined	0.196
r_nbtor_refined	0.194
r_symmetry_xyhbond_nbd_other	0.141
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.067
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.007
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4499
Nucleic Acid Atoms	360
Solvent Atoms	146
Heterogen Atoms	21

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
pointless	data scaling
PHASER	phasing