2ONA | pdb_00002ona

MVGGVV peptide derived from Alzheimer's A-beta, residues 35-40

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		polyalanine idealized beta strand

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	30 mg/mL peptide in water mixed 1:1 with reservoir containing 0.02 M CaCl2, 30% MPD, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 25.862	α = 77.18
b = 9.699	β = 74.69
c = 15.851	γ = 86.93

Symmetry
Space Group	P 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		2005-12-18	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	2	90	90.2	0.16	10.2	1.6		409		-3	25.4

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)
	2	2.15	94.2		0.222		1.6	163

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	polyalanine idealized beta strand	2.03	24.94	409	44		0.211	0.202	0.21	0.264	0.29	RANDOM	10.788

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]
-0.1	-0.28	0.26	0.1	-0.07	-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.457
r_scangle_it	2.628
r_dihedral_angle_1_deg	2.56
r_scbond_it	2.08
r_mcangle_it	1.821
r_mcbond_it	1.732
r_angle_refined_deg	1.254
r_angle_other_deg	0.669
r_mcbond_other	0.456
r_symmetry_vdw_refined	0.23
r_nbd_other	0.18
r_symmetry_vdw_other	0.177
r_nbd_refined	0.159
r_xyhbond_nbd_refined	0.145
r_nbtor_refined	0.14
r_symmetry_hbond_refined	0.096
r_nbtor_other	0.085
r_chiral_restr	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	152
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms

Software

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