7Z60 | pdb_00007z60

Human transthyretin (TTR) complexed with Quercetin 3-O-beta-D-galactoside

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Protein: 5 mg/ml TTR dialysed against 0.1 M NaCl, 0.05M Na acetate, pH 5.5. Precipitant:80% (30% PEG 4000, 0.2 M Imidazole Malate pH 6.0), 15% ((12% MPEG 5000, 0.1 Sodium Acetate pH 5.5)

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.23	α = 90
b = 85.6	β = 90
c = 64.43	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 EIGER X 9M		2016-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.980	SOLEIL	PROXIMA 2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	42.8	99.7	0.99	18.1	6.8		45603

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.43			0.39

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4PMF	1.4	42.8	45603	2401	99.7	0.1841	0.1823	0.2197	0.246	RANDOM	27.601

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]
0.01			-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.945
r_dihedral_angle_4_deg	20.914
r_dihedral_angle_3_deg	14.573
r_dihedral_angle_1_deg	6.766
r_angle_refined_deg	1.758
r_angle_other_deg	1.439
r_chiral_restr	0.086
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1785
Nucleic Acid Atoms
Solvent Atoms	195
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing