2QGB

Human transthyretin (TTR) in Apo-form

X-RAY DIFFRACTION

---

Starting Model(s)

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

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., VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.33	42.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.85	α = 90
b = 85.398	β = 90
c = 64.351	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); single crystal Si(111) bent monochromator (ho rizontal focusing)	2007-01-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.9791	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	1.4	50	99.9	0.045	13.9	6.8		47065			16.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.43	100		0.459	4.5	4.2	6.7	3090

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Human Transthyretin PDB 2FBR	1.4	50	44643	47021	2378	99.38	0.167	0.166	0.188	RANDOM	13.715

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]
-0.11			-0.21		0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.472
r_dihedral_angle_4_deg	17.038
r_dihedral_angle_3_deg	13.126
r_sphericity_free	10.327
r_dihedral_angle_1_deg	6.014
r_scangle_it	5.471
r_sphericity_bonded	4.818
r_scbond_it	4.331
r_mcangle_it	3.074
r_mcbond_it	2.613
r_rigid_bond_restr	2.199
r_angle_refined_deg	1.826
r_angle_other_deg	0.972
r_mcbond_other	0.968
r_nbd_refined	0.213
r_nbd_other	0.206
r_nbtor_refined	0.182
r_symmetry_vdw_other	0.177
r_symmetry_vdw_refined	0.163
r_xyhbond_nbd_refined	0.123
r_chiral_restr	0.113
r_nbtor_other	0.091
r_symmetry_hbond_refined	0.063
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1773
Nucleic Acid Atoms
Solvent Atoms	166
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
PHASER	phasing