5E4A | pdb_00005e4a

Human transthyretin (TTR) complexed with (2,7-Dichloro-fluoren-9-ylideneaminooxy)-acetic acid.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4TQ8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	Protein: TTR at 5 mg/ml + 1.6 milli-M inhibitor. Precipitant: 18% PEG4K, 0.08M imidazole malate, pH 6.0 and 13.5% PEG10K, 0.06M ammonium acetate, pH 4.5 Cryoprotectant: 10% diethylene glycol + 5% MPD + 15% 2,3-butanediol + 5% 1,4-dioxane, 25% MPEG 5K, 0.1 M mixed (Na acetate, ADA, Bicine - 60% at pH 4/40% at pH 10) 1 milli-M inhibitor.

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.21	α = 90
b = 85.99	β = 90
c = 63.82	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	PIXEL	DECTRIS PILATUS 6M-F	mirrors	2014-01-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.87006	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.33	43.21	99.9	0.076	0.072	14.92	9.12	55430	55377		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.33	1.36	99.9		1.86	1.22	9.23

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	4TQ8	1.33	42.99	52608	2769	99.9	0.14202	0.13944	0.14	0.19239	0.19	RANDOM	24.215

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]
-0.69			0.31		0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	45.611
r_dihedral_angle_2_deg	30.932
r_sphericity_bonded	18.658
r_dihedral_angle_4_deg	15.784
r_dihedral_angle_3_deg	15.012
r_rigid_bond_restr	7.789
r_dihedral_angle_1_deg	6.624
r_long_range_B_refined	6.244
r_scbond_it	4.285
r_mcangle_it	3.625
r_mcbond_it	2.867
r_angle_refined_deg	2.452
r_chiral_restr	0.188
r_bond_refined_d	0.028
r_gen_planes_refined	0.015
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1793
Nucleic Acid Atoms
Solvent Atoms	267
Heterogen Atoms	21

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
Coot	model building