4TQP | pdb_00004tqp

Human transthyretin (TTR) complexed with (R)-3-(9H-fluoren-9-ylideneaminooxy)-2-methyl-N-(methylsulfonyl) propionamide in a dual binding mode

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.7	293	Protein: 5 mg/ml in 0.05 M NaCl, 0.05 M sodium acetate, pH 5.5. Precipitant: 60% (30% PEG-4K, 0.2 M imidazole malate, pH 6.0) and 40% (MPEG-5K, 0.1 M sodium acetate, pH 5.5). Cryoprotectant: 40% (25 % diethylene glycol, 12.5 % MPD, 37.5 % 2,3-butanediol, 12.5 % 1,4-dioxane), 12.5% MPEG 5K, 25% MPEG 550, 0.1 M (sodium propionate, sodium cacodylate, Bis-Tris-propane: 50% component A pH 4; 50% B pH 9.5) with 1 milli-M ligand.

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.121	α = 90
b = 86.081	β = 90
c = 63.473	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 6M-F		2014-01-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.87006	ESRF	ID23-1

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	1.58	51.1	99.9	0.125	0.118	14.12	9.19	33125	33100		-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	1.58	1.64	99.9		1.87	9.5

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	4TQI	1.58	51.09	31425	1674	99.92	0.14441	0.14148	0.1385	0.19761	0.1961	RANDOM	19.98

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]
0.19			-0.21		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.429
r_dihedral_angle_4_deg	18.643
r_dihedral_angle_3_deg	14.398
r_scangle_it	7.776
r_dihedral_angle_1_deg	6.799
r_scbond_it	5.449
r_mcangle_it	4.253
r_rigid_bond_restr	2.867
r_mcbond_it	2.728
r_angle_refined_deg	2.15
r_chiral_restr	0.157
r_bond_refined_d	0.023
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_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1792
Nucleic Acid Atoms
Solvent Atoms	260
Heterogen Atoms	62

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building
XDS	data scaling
XSCALE	data scaling
ADSC	data collection