6DIY | pdb_00006diy

YTFGQ segment from Human Immunoglobulin Light-Chain Variable Domain, Residues 96-100, assembled as an amyloid fibril

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	0.1 M Bis-Tris propane, 2.8 M Sodium Acetate

Crystal Properties
Matthews coefficient	Solvent content
1.31	6.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.78	α = 90
b = 4.81	β = 104.95
c = 18.91	γ = 90

Symmetry
Space Group	C 1 2 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 PILATUS 6M-F		2015-11-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.885600	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	0.89	18.27	90.7	0.062	0.068	0.999	14.11	5.104		2477			7.31

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.89	0.92	49.8		0.218	0.258	0.942	3.15	3

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	AB INITIO PHASING	THROUGHOUT	NO Starting model, We used DIRECT METHODS	0.9	18.27	2228	248	90.83	0.0993	0.0971	0.1	0.1198	0.13	RANDOM	5.236

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]
-0.23		0.01	-0.02		0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	9.694
r_sphericity_bonded	7.013
r_dihedral_angle_3_deg	5.077
r_dihedral_angle_1_deg	4.457
r_angle_refined_deg	1.438
r_rigid_bond_restr	1.09
r_angle_other_deg	0.684
r_chiral_restr	0.161
r_bond_refined_d	0.013
r_gen_planes_refined	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	9.694
r_sphericity_bonded	7.013
r_dihedral_angle_3_deg	5.077
r_dihedral_angle_1_deg	4.457
r_angle_refined_deg	1.438
r_rigid_bond_restr	1.09
r_angle_other_deg	0.684
r_chiral_restr	0.161
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	44
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	13

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SHELXD	phasing

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.