1JVK | pdb_00001jvk

THREE-DIMENSIONAL STRUCTURE OF AN IMMUNOGLOBULIN LIGHT CHAIN DIMER ACTING AS A LETHAL AMYLOID PRECURSOR

X-RAY DIFFRACTION

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.28	α = 90
b = 83.32	β = 90
c = 112.591	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV		2000-05-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	1.94	19.8	98.1	0.04	29.6	4	32131				30.46

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)
	1.94	2.01	89.1		0.319	3.78

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1.94	19.8	33848	32131	1717	100	0.223	0.22309	0.22137	0.23	0.25409	0.26	RANDOM	30.188

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]
-0.86			-0.15		1.01

RMS Deviations
Key	Refinement Restraint Deviation
p_scangle_it	4.43
p_scbond_it	2.894
p_mcangle_it	2.254
p_angle_d	1.942
p_mcbond_it	1.278
p_hb_or_metal_coord	0.246
p_xhyhbond_nbd	0.246
p_xyhbond_nbd	0.2
p_chiral_restr	0.116
p_bond_d	0.02

RMS Deviations
Key	Refinement Restraint Deviation
p_scangle_it	4.43
p_scbond_it	2.894
p_mcangle_it	2.254
p_angle_d	1.942
p_mcbond_it	1.278
p_hb_or_metal_coord	0.246
p_xhyhbond_nbd	0.246
p_xyhbond_nbd	0.2
p_chiral_restr	0.116
p_bond_d	0.02
p_planar_d	0.008
p_plane_restr	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3167
Nucleic Acid Atoms
Solvent Atoms	251
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

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.