8SDJ | pdb_00008sdj

Hydrophobic Interactions Drive the Tetrameric Assembly of the TRIM20 Coiled-Coil Domain

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8SDE	one chain of TRIM29 structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	298	0.1M HEPES pH8.0, 35% 1,2-Propanediol, 10% PEG400

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.6	α = 90
b = 38.83	β = 89.94
c = 164.3	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	PIXEL	DECTRIS EIGER X 16M		2020-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.97918	APS	24-ID-E

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	2.4	9	95.7	0.033	0.999	13.6	2.9		18553

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	2.4	2.53	94.3		0.169	0.991	4	2.7

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.4	9	18548	838	95.094	0.261	0.259	0.26	0.294	0.29	75.81

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]
5.141		0.154	5.94		-11.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.54
r_dihedral_angle_3_deg	21.703
r_dihedral_angle_4_deg	17.439
r_lrange_it	16.773
r_scangle_it	15.12
r_mcangle_it	10.727
r_scbond_it	10.67
r_mcbond_it	7.763
r_dihedral_angle_1_deg	5.592
r_angle_refined_deg	1.702

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.54
r_dihedral_angle_3_deg	21.703
r_dihedral_angle_4_deg	17.439
r_lrange_it	16.773
r_scangle_it	15.12
r_mcangle_it	10.727
r_scbond_it	10.67
r_mcbond_it	7.763
r_dihedral_angle_1_deg	5.592
r_angle_refined_deg	1.702
r_nbtor_refined	0.312
r_symmetry_nbd_refined	0.293
r_nbd_refined	0.255
r_symmetry_xyhbond_nbd_refined	0.198
r_xyhbond_nbd_refined	0.166
r_chiral_restr	0.135
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3636
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	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.