3IPE | pdb_00003ipe

Human Transthyretin (TTR) complexed with a palindromic bivalent amyloid inhibitor (7 carbon linker).

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ROX	PDB ENTRY 2ROX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.5	298	25- 32% v/v PEG550-monomethyl ether, 70 mM NaAc buffer pH 4-5 and 100 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.241	α = 90
b = 84.876	β = 90
c = 63.39	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	CCD	ADSC		2006-09-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	1.4	43	98.1	0.062	16.5	7.4		45900		2	16.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.4	1.48	90.3

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	PDB ENTRY 2ROX	1.4	35.26	43546	2317	98.1	0.176	0.175	0.18	0.196	0.2	RANDOM	16.27

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]
0.09			-0.01		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.118
r_dihedral_angle_4_deg	19.311
r_dihedral_angle_3_deg	13.693
r_dihedral_angle_1_deg	5.862
r_scangle_it	5.109
r_scbond_it	3.231
r_mcangle_it	2.393
r_angle_refined_deg	1.382
r_mcbond_it	1.342
r_rigid_bond_restr	1.313
r_angle_other_deg	0.791
r_mcbond_other	0.331
r_chiral_restr	0.079
r_bond_refined_d	0.01
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_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1778
Nucleic Acid Atoms
Solvent Atoms	138
Heterogen Atoms	45

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling