3GLZ | pdb_00003glz

Human Transthyretin (TTR) complexed with(E)-3-(2-(trifluoromethyl)benzylideneaminooxy)propanoic acid (inhibitor 11)

X-RAY DIFFRACTION

---

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	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. TTR:ligand complexes were prepared from crystals soaked with a tenfold molar excess of ligand for more than two weeks., VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.181	α = 90
b = 84.939	β = 90
c = 63.422	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++	mirrors	2007-02-05	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	63.37	99.71			22460	22460

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	99.94

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	18.45	22460	22460	1149	99.71	0.22668	0.22668	0.22417	0.28	0.27349	0.32	RANDOM	31.604

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]
0.47			-0.62		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.839
r_dihedral_angle_4_deg	21.177
r_dihedral_angle_3_deg	16.396
r_dihedral_angle_1_deg	5.942
r_scangle_it	3.223
r_scbond_it	2.42
r_angle_refined_deg	1.759
r_mcangle_it	1.313
r_mcbond_it	0.877
r_nbtor_refined	0.313
r_symmetry_vdw_refined	0.235
r_nbd_refined	0.21
r_xyhbond_nbd_refined	0.137
r_symmetry_hbond_refined	0.111
r_chiral_restr	0.105
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1709
Nucleic Acid Atoms
Solvent Atoms	158
Heterogen Atoms	36

Software

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