4IVH | pdb_00004ivh

Crystal structure of QKLVFFAED nonapeptide segment from amyloid beta incorporated into a macrocyclic beta-sheet template

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	298	0.5M Sodium citrate tribasic dihydrate, 35% tert-butanol, 1% PEG 3350 98K, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.085	α = 90
b = 45.085	β = 90
c = 29.247	γ = 120

Symmetry
Space Group	P 6 2 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	ADSC QUANTUM 315r		2012-10-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	0.92	ALS	8.2.1

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	1.77	50	99	0.123	0.123	22	20	38242	1909		-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	1.77	1.83	100		0.456		17.8	178

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.77	29.26	1779	130	98.71	0.22759	0.22422	0.25	0.27056	0.31	RANDOM	42.122

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]
0.21	0.21		0.21		-0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	20.748
r_dihedral_angle_3_deg	16.349
r_dihedral_angle_1_deg	6.893
p_mcangle_it	6.268
r_mcbond_it	4.108
r_mcbond_other	3.647
r_angle_refined_deg	2.96
r_angle_other_deg	1.96
r_chiral_restr	0.128
r_bond_refined_d	0.031

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	20.748
r_dihedral_angle_3_deg	16.349
r_dihedral_angle_1_deg	6.893
p_mcangle_it	6.268
r_mcbond_it	4.108
r_mcbond_other	3.647
r_angle_refined_deg	2.96
r_angle_other_deg	1.96
r_chiral_restr	0.128
r_bond_refined_d	0.031
r_gen_planes_refined	0.027
r_bond_other_d	0.024
r_gen_planes_other	0.018

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	155
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	6

Software

Software
Software Name	Purpose
HKL-2000	data collection
AutoSol	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.