3B56 | pdb_00003b56

Crystal structure of transthyretin in complex with 3,5-diiodosalicylic acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F86	PDB ENTRY 1F86

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	287	200mM acetate buffer, 2.2M ammonium sulfate, 7% glycerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.539	α = 90
b = 85.757	β = 90
c = 64.346	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	MARRESEARCH		2005-03-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.55	28.58	99.9	0.052	15.2	3.6	34993	34958		2

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 1F86	1.55	27.34	33166	1756	99.91	0.19043	0.18917	0.1874	0.21368	0.2104	RANDOM	14.518

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]
0.14			-0.39		0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.567
r_dihedral_angle_4_deg	17.553
r_dihedral_angle_3_deg	12.139
r_dihedral_angle_1_deg	5.551
r_scangle_it	3.281
r_scbond_it	2.105
r_mcangle_it	1.49
r_angle_refined_deg	1.271
r_mcbond_it	0.789
r_nbtor_refined	0.31
r_symmetry_vdw_refined	0.285
r_nbd_refined	0.202
r_symmetry_hbond_refined	0.153
r_xyhbond_nbd_refined	0.132
r_chiral_restr	0.079
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1786
Nucleic Acid Atoms
Solvent Atoms	189
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
DNA	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing