5WHP | pdb_00005whp

Crystal structure of the segment, NFGTFS, from the A315T familial variant of the low complexity domain of TDP-43, residues 312-317

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	100mM sodium acetate 4.6, 200mM ammonium acetate, 30% PEG 4000

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 15.33	α = 90
b = 4.84	β = 96.91
c = 23.57	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	CCD	ADSC QUANTUM 315		2014-10-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.9791	APS	24-ID-E

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	15.22	87.6	0.086	0.096	0.993	14.97	4.918		1823		-3	4.863

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	1.03	37		0.104	0.125	0.98	7.59	2.842

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	AB INITIO PHASING	THROUGHOUT	1	15.22	1639	183	87.68	0.0873	0.0866	0.09	0.0929	0.09	RANDOM	2.626

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]
0.19		-0.17	0.07		-0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	14.007
r_dihedral_angle_3_deg	8.865
r_rigid_bond_restr	5.773
r_dihedral_angle_1_deg	4.212
r_sphericity_bonded	2.03
r_angle_refined_deg	1.79
r_angle_other_deg	0.687
r_chiral_restr	0.132
r_bond_refined_d	0.019
r_gen_planes_refined	0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	14.007
r_dihedral_angle_3_deg	8.865
r_rigid_bond_restr	5.773
r_dihedral_angle_1_deg	4.212
r_sphericity_bonded	2.03
r_angle_refined_deg	1.79
r_angle_other_deg	0.687
r_chiral_restr	0.132
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	48
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms

Software

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

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.