6DIX | pdb_00006dix

NFVFGT segment from Human Immunoglobulin Light-Chain Variable Domain, Residues 98-103, assembled as an amyloid fibril

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	0.1 M Imidazole, 20% PEG 3000, 0.2 M Zinc Acetate

Crystal Properties
Matthews coefficient	Solvent content
1.46	15.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 16.03	α = 90.89
b = 11.66	β = 103.23
c = 21.94	γ = 90.26

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	PIXEL	DECTRIS PILATUS 6M-F		2015-03-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.9717	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	1	21.35	81.8	0.066	0.077	0.997	12.83	3.424		6835			8.571

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	1	1.07	60.4		0.124	0.148	0.982	6.73	3.177

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	1	21.35	6154	684	81.83	0.1048	0.1025	0.11	0.1247	0.13	RANDOM	7.488

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]
-0.38	-0.24	-0.18	-0.03	-0.02	0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.969
r_rigid_bond_restr	20.279
r_sphericity_free	17.741
r_dihedral_angle_3_deg	12.47
r_dihedral_angle_1_deg	8.046
r_sphericity_bonded	6.447
r_angle_refined_deg	1.589
r_angle_other_deg	1.477
r_chiral_restr	0.086
r_gen_planes_other	0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.969
r_rigid_bond_restr	20.279
r_sphericity_free	17.741
r_dihedral_angle_3_deg	12.47
r_dihedral_angle_1_deg	8.046
r_sphericity_bonded	6.447
r_angle_refined_deg	1.589
r_angle_other_deg	1.477
r_chiral_restr	0.086
r_gen_planes_other	0.01
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	196
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
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.