2ON9 | pdb_00002on9

Structure of an amyloid forming peptide VQIVYK from the repeat region of Tau

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		geometrically idealized b-strands

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	Peptide concentration: 30mg/ml, peptide:Reservoir ratio 1:1, Reservoir: 0.2M Ammonium acetate, 0.1M HEPES-Na, 45% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
1.53	19.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 4.863	α = 90
b = 61.926	β = 98.11
c = 15.413	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MAR CCD 165 mm		2005-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID13		ESRF	ID13

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.5	90	85.4	0.161	3.8	2.89		1222

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)
	1.5	1.62	77		0.489			238

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	Extended beta strand VQIVYK	1.51	30.96	1207	59	85.06	0.207	0.206	0.21	0.225	0.21	RANDOM	8.391

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]
0.08		0.03	-0.14		0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	44.032
r_dihedral_angle_3_deg	11.4
r_dihedral_angle_1_deg	4.252
r_scangle_it	1.332
r_angle_refined_deg	1.197
r_scbond_it	1.11
r_mcangle_it	0.761
r_angle_other_deg	0.757
r_mcbond_it	0.62
r_xyhbond_nbd_refined	0.239
r_nbtor_refined	0.183
r_nbd_other	0.178
r_symmetry_vdw_other	0.177
r_symmetry_hbond_refined	0.143
r_mcbond_other	0.122
r_symmetry_vdw_refined	0.121
r_chiral_restr	0.092
r_nbtor_other	0.071
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_nbd_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	111
Nucleic Acid Atoms
Solvent Atoms	7
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction