3TCT | pdb_00003tct

Structure of wild-type TTR in complex with tafamidis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2FBR	pdb entry 2FBR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5		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 WITH INHIBITORS 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, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.12	42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.749	α = 90
b = 84.994	β = 90
c = 64.334	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		CCD	MARMOSAIC 325 mm CCD	FLAT MIRROR (VERTICAL FOCUSING)	2010-02-19	M	SINGLE WAVELENGTH
2	1	x-ray				SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HO RIZONTAL FOCUSING)		M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.9795	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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
1,2	1.3	50	99.4	0.035	51.5	7		58308			16.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	1.3	1.35	96.5		0.63	2.4	5.8

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 2FBR	1.3	50	58122	2940	99.4	0.163	0.161	0.17	0.192	0.2	RANDOM	20.4

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]
0.1			-0.28		0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.514
r_dihedral_angle_4_deg	17.973
r_dihedral_angle_3_deg	15.022
r_sphericity_free	9.843
r_scangle_it	6.206
r_dihedral_angle_1_deg	5.993
r_sphericity_bonded	5.349
r_scbond_it	4.189
r_mcangle_it	3.198
r_mcbond_it	2.078
r_rigid_bond_restr	2.056
r_angle_refined_deg	1.682
r_angle_other_deg	1.559
r_mcbond_other	1.024
r_chiral_restr	0.109
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.003
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1773
Nucleic Acid Atoms
Solvent Atoms	141
Heterogen Atoms	40

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling