11KP | pdb_000011kp

Crystal structure of the Caenorhabditis elegans telomeric POT-1-TEBP-1 complex interface

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-P42001-F1	used only part of the model, from amino acids 1-171

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.75	289	SeMet-substituted complex (17 mg/ml) was mixed 1:1 with the well solution 100 mM MES (pH 6.75), 100 mM NaCl, and 8% PEG 3350. Crystals were harvested in 20 mM Tris (pH 8.0), 100 mM MES (pH 6.5), 200 mM NaCl, 10% PEG 3350, and cryoprotected in harvesting solution with 35% ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.799	α = 90
b = 39.81	β = 97.027
c = 103.941	γ = 90

Symmetry
Space Group	I 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 EIGER2 X 9M		2021-09-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.97158	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.47	63.5	96.5	0.085	0.997	10.2	6.7		94669			19.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.47	1.5			0.603	0.878

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.48	51.58	1.36	94642	4668	95.7	0.1847	0.1833	0.1834	0.2107	0.2099	29.91

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.2098
f_angle_d	0.8295
f_chiral_restr	0.0724
f_bond_d	0.006
f_plane_restr	0.0057

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2203
Nucleic Acid Atoms
Solvent Atoms	321
Heterogen Atoms

Software

Software
Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
AutoSol	phasing
PHENIX	refinement
Coot	model building