3IMS | pdb_00003ims

Transthyretin in complex with 2,6-dibromo-4-(2,6-dichlorophenethyl)phenol

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QGB	pdb entry 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, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.5	α = 90
b = 85.11	β = 90
c = 63.321	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)	2006-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.9797	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	63.37	99.7	0.04	26.1	3.6		45887			17.1

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 2QGB	1.4	50	43555	2332	99.67	0.167	0.165	0.17	0.197	0.2	RANDOM	18.912

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]
0.2			-0.44		0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.899
r_dihedral_angle_4_deg	18.442
r_dihedral_angle_3_deg	13.619
r_sphericity_free	9.872
r_dihedral_angle_1_deg	6.135
r_scangle_it	5.364
r_sphericity_bonded	4.559
r_scbond_it	4.341
r_mcangle_it	2.861
r_rigid_bond_restr	2.562
r_mcbond_it	2.454
r_angle_refined_deg	1.741
r_angle_other_deg	0.935
r_mcbond_other	0.87
r_symmetry_vdw_refined	0.235
r_nbd_refined	0.224
r_nbd_other	0.2
r_symmetry_vdw_other	0.19
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.17
r_symmetry_hbond_refined	0.151
r_chiral_restr	0.111
r_nbtor_other	0.089
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1872
Nucleic Acid Atoms
Solvent Atoms	148
Heterogen Atoms	38

Software

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