3IMR | pdb_00003imr

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

X-RAY DIFFRACTION

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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
2.14	42.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.927	α = 90
b = 85.002	β = 90
c = 64.506	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 collimating mirror, double crystal monochromator, toroid focusing mirror		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.9194	SSRL	BL9-2

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	1.7	64.55	99.5	0.057	34.6	14		26903			23.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.7	1.76	97		0.695	7.3	11.9	2588

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	1.7	50	26562	1333	99.56	0.172	0.169	0.18	0.217	0.22	RANDOM	27.504

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]
1.18			-0.72		-0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.117
r_dihedral_angle_4_deg	17.51
r_dihedral_angle_3_deg	14.69
r_sphericity_free	10.749
r_dihedral_angle_1_deg	5.988
r_scangle_it	5.86
r_sphericity_bonded	5.544
r_rigid_bond_restr	5.136
r_scbond_it	4.646
r_mcangle_it	3.06
r_mcbond_it	2.563
r_angle_refined_deg	1.818
r_angle_other_deg	0.927
r_mcbond_other	0.921
r_nbd_other	0.203
r_nbd_refined	0.196
r_symmetry_vdw_refined	0.191
r_nbtor_refined	0.186
r_symmetry_hbond_refined	0.183
r_symmetry_vdw_other	0.168
r_xyhbond_nbd_refined	0.163
r_chiral_restr	0.109
r_nbtor_other	0.092
r_bond_refined_d	0.019
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1863
Nucleic Acid Atoms
Solvent Atoms	85
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