3GS4 | pdb_00003gs4

Human transthyretin (TTR) complexed with 3-(9H-fluoren-9-ylideneaminooxy)propanoic acid (inhibitor 15)

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	290	Crystals of wt-TTR were obtained from 5-7 mg/mL protein solutions (in 100 mM KCl, 1 mM EDTA, 10 mM sodium phosphate, pH 7.0, 0.3 M ammonium sulfate) equilibrated against 2 M ammonium sulfate in hanging drops. All TTR:ligand complexes were prepared from crystals soaked with a ten fold molar excess of ligand for more than three weeks. , VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.185	α = 90
b = 85.726	β = 90
c = 64.775	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	120	IMAGE PLATE	RIGAKU RAXIS IV++		2007-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	1.78	17.61	99.65			23671	23671

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.78	1.826	100

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1BMZ	1.78	17.61	23671	22457	1214	99.65	0.22769	0.22769	0.22506	0.27	0.27818	0.31	RANDOM	32.855

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]
0.5			-0.61		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.041
r_dihedral_angle_4_deg	23.103
r_dihedral_angle_3_deg	15.138
r_dihedral_angle_1_deg	5.628
r_scangle_it	3.523
r_scbond_it	2.266
r_angle_refined_deg	1.779
r_mcangle_it	1.388
r_mcbond_it	0.838
r_nbtor_refined	0.313
r_symmetry_vdw_refined	0.293
r_nbd_refined	0.215
r_symmetry_hbond_refined	0.163
r_xyhbond_nbd_refined	0.151
r_chiral_restr	0.108
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1752
Nucleic Acid Atoms
Solvent Atoms	181
Heterogen Atoms	40

Software

Software
Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling