4YDM | pdb_00004ydm

High resolution crystal structure of human transthyretin bound to ligand and conjugates of 3-(5-(3,5-dichloro-4-hydroxyphenyl)-1,3,4-oxadiazol-2-yl)phenyl fluorosulfate

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	298	The WT-TTR was concentrated to 4 mg/mL in 10 mM NaPi, 100 mM KCl, at pH 7.6 and co-crystallized at room temperature using the vapor-diffusion sitting drop method. Crystals were grown from 1.395 M sodium citrate, 3.5% v/v glycerol at pH 5.5. The crystals were frozen using a cryo-protectant solution of 1.395 M sodium citrate, pH 5.5, containing 10% v/v glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.27	41.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.709	α = 90
b = 85.42	β = 90
c = 63.537	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	PSI PILATUS 6M		2014-01-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97945	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.25	38.2	99.1	0.029	0.032	0.013	25.5	6.3	64492	64492

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.25	1.32	95.8		0.498	0.498	0.215	1.6	6.2	8993

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	2qgb	1.25	63.54	61174	3263	98.99	0.1471	0.14575	0.15	0.17232	0.18	RANDOM	20.421

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]
-0.94			0.85		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	59.37
r_dihedral_angle_2_deg	31.893
r_dihedral_angle_4_deg	19.002
r_dihedral_angle_3_deg	14.08
r_sphericity_bonded	13.42
r_long_range_B_refined	7.438
r_long_range_B_other	7.437
r_rigid_bond_restr	6.56
r_dihedral_angle_1_deg	6.095
r_scangle_other	4.146
r_scbond_it	3.693
r_scbond_other	3.692
r_angle_other_deg	2.97
r_mcangle_other	2.707
r_mcangle_it	2.692
r_mcbond_it	2.086
r_mcbond_other	2.024
r_angle_refined_deg	1.738
r_chiral_restr	0.101
r_bond_refined_d	0.015
r_gen_planes_other	0.014
r_gen_planes_refined	0.011
r_bond_other_d
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_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1793
Nucleic Acid Atoms
Solvent Atoms	197
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction