2FBR | pdb_00002fbr

Human transthyretin (TTR) complexed with bivalant amyloid inhibitor (4 carbon linker)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BMZ	PDB ENTRY 1BMZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	289	TTR bivalent inhibitor complexes of 1:1 stoichiometry resulting from coassembly at 5-7 mg/mL (95-133 microM in 100 mM KCl, 1 mM EDTA, 10 mM sodium phosphate, 0.35-0.50 M ammonium sulfate equilibrated against 2 M ammonium sulfate, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.599	α = 90
b = 84.355	β = 90
c = 65.569	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	SBC-3		2002-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97918	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.46	42.26	97.73			38794	38794	38794

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	1.46	1.498	94

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 (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1BMZ	1.46	42.26	38794	2062	97.73	0.21076	0.21076	0.21005	0.22356	RANDOM	17.399

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]
-0.77			0.11		0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.225
r_scangle_it	4.851
r_scbond_it	3.01
r_mcangle_it	2.167
r_angle_refined_deg	1.721
r_angle_other_deg	1.488
r_mcbond_it	1.196
r_symmetry_vdw_other	0.306
r_nbd_other	0.267
r_nbd_refined	0.198
r_xyhbond_nbd_refined	0.161
r_symmetry_hbond_refined	0.146
r_symmetry_vdw_refined	0.129
r_chiral_restr	0.126
r_nbtor_other	0.087
r_bond_refined_d	0.018
r_bond_other_d	0.014
r_gen_planes_refined	0.01
r_gen_planes_other	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1770
Nucleic Acid Atoms
Solvent Atoms	181
Heterogen Atoms	37

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
EPMR	phasing