2ONV | pdb_00002onv

Crystal Structure of the amyloid-fibril forming peptide GGVVIA derived from the Alzheimer's amyloid Abeta (Abeta37-42).

X-RAY DIFFRACTION

---

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		291	Peptide concentration: 15.0 mg/ml, Peptide:reservoir:additive ratio 5:4:1, Reservoir: 2.0M Ammonium sulfate, Additive: 3.0% 0.1M hexamine cobalt (III) chloride , VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
1.6	23.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 16.76	α = 90
b = 41.134	β = 90
c = 4.789	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	CCD	MAR CCD 165 mm		2005-12-17	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	1.6	90	96.7	0.192	12.6	4.5		532			15.962

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)
	1.6	1.72	96.7		0.42		4.9	87

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 GGVVIA	1.61	20.57	515	51	96.44	0.235	0.228	0.24	0.299	0.32	RANDOM	9.99

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]
0.7			0.89		-1.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	8.031
r_angle_refined_deg	1.859
r_mcangle_it	1.773
r_dihedral_angle_3_deg	1.738
r_mcbond_it	1.388
r_angle_other_deg	1.041
r_scangle_it	0.89
r_scbond_it	0.651
r_xyhbond_nbd_refined	0.352
r_symmetry_vdw_other	0.273
r_nbd_other	0.182
r_symmetry_vdw_refined	0.16
r_nbtor_refined	0.158
r_symmetry_hbond_refined	0.148
r_mcbond_other	0.137
r_chiral_restr	0.084
r_nbtor_other	0.078
r_nbd_refined	0.026
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	36
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms

Software

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