9JBL | pdb_00009jbl

Crystal structure of amyloidogenic peptide Bz-FFAALL-NH2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7N8R	Polyalanine model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION		298	Formic acid

Crystal Properties
Matthews coefficient	Solvent content
1.52	19.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 4.813	α = 90
b = 32.067	β = 99.24
c = 13.478	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	PIXEL	DECTRIS EIGER X 4M		2023-07-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	1.000	SPring-8	BL26B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	32.07	99.2	0.052	0.062	0.033	0.999	25.6	6.3		2196

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1	1.05	97.9		0.063	0.078	0.045	0.995		5.3

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	MOLECULAR REPLACEMENT	THROUGHOUT	1	16.03	2055	125	99.09	0.03653	0.03602	0.068	0.04439	0.0691	RANDOM	2.97

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]
-0.41		0.49	0.07		0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	9.52
r_dihedral_angle_3_deg	7.779
r_rigid_bond_restr	5.399
r_dihedral_angle_1_deg	4.421
r_angle_refined_deg	1.555
r_angle_other_deg	1.322
r_long_range_B_refined	0.641
r_long_range_B_other	0.636
r_scangle_other	0.559
r_mcbond_it	0.506
r_mcangle_it	0.5
r_mcangle_other	0.497
r_mcbond_other	0.482
r_scbond_it	0.474
r_scbond_other	0.469
r_chiral_restr	0.063
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	49
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	8

Software

Software
Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building
REFMAC	refinement