4TQ8 | pdb_00004tq8

Dual binding mode for 3-(9H-fluoren-9-ylideneaminooxy)propanoic acid binding to Human transthyretin (TTR)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.7	293	Protein: 5 mg/ml 1 milli-M ligand Precipitant: 60% (30% PEG-4K, 0.2 M imidazole malate, pH 6.0) 40% (24% MPEG-5K, 0.1 M sodium acetate, pH 5.5) Drops: 1 micro-L protein-ligand complex 1 micro-L precipitant. Cryoprotectant:: 40% (12.5 % diethylene glycol + 12.5 % ethylene glycol + 12.5 % glycerol + 12.5 % 1,2-propanediol + 12.5 % DMSO + 12.5 % 1,4-dioxane), 25% MPEG 5K, 0.1 M sodium propionate, sodium cacodylate, Bis-Tris-propane(65% component A pH 4; 35% B pH 9.5 and 1 milli-M ligand.

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.14	α = 90
b = 86.04	β = 90
c = 63.48	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	DECTRIS PILATUS 2M-F		2014-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8729	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.52	43.1	99.8	0.145	0.137	11.9	8.73	37141	37078		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.52	1.61	98.8		1.01	7.3

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	1.52	38.56	35223	1854	99.84	0.18728	0.18605	0.18	0.2098	0.21	RANDOM	22.219

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]
0.51			-0.54		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.192
r_dihedral_angle_3_deg	14.879
r_dihedral_angle_4_deg	13.451
r_dihedral_angle_1_deg	6.064
r_angle_refined_deg	2.112
r_chiral_restr	0.15
r_bond_refined_d	0.022
r_gen_planes_refined	0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1794
Nucleic Acid Atoms
Solvent Atoms	232
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building
XDS	data scaling
MOLREP	phasing
MxCuBE	data collection