3A4D

Crystal structure of Human Transthyretin (wild-type)

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, SITTING DROP	5.3	293	200mM citrate, 3M ammonium sulfate, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.84	α = 90
b = 43.084	β = 90
c = 64.29	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	ADSC QUANTUM 270		2006-12-23

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	1.0	Photon Factory	BL-17A

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	2	50		0.095	36.2			16752

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1BMZ	2	33.04	15872	846	99.79	0.17071	0.16783	0.22856	RANDOM	17.559

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			0.1		0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.577
r_dihedral_angle_4_deg	21.142
r_dihedral_angle_3_deg	18.066
r_dihedral_angle_1_deg	7.26
r_scangle_it	6.131
r_scbond_it	3.923
r_mcangle_it	2.464
r_angle_refined_deg	2.068
r_mcbond_it	1.739
r_nbtor_refined	0.319
r_symmetry_vdw_refined	0.232
r_nbd_refined	0.21
r_xyhbond_nbd_refined	0.18
r_symmetry_hbond_refined	0.175
r_chiral_restr	0.166
r_bond_refined_d	0.026
r_gen_planes_refined	0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1785
Nucleic Acid Atoms
Solvent Atoms	121
Heterogen Atoms	28

Software

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