9R9B | pdb_00009r9b

Crystal structure of clathrin heavy chain in complex with a peptidomimetic inhibitor of the TACC3 interaction

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5ODS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.3	291	20% w/v polyethylene glycol 3350 200 mM tri-potassium citrate

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.218	α = 90
b = 111.218	β = 90
c = 212.862	γ = 120

Symmetry
Space Group	P 61 2 2

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 XE 16M		2023-07-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.95373	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.146	96.318	96.1	0.984	23	39.5		24209

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.146	2.419			0.785

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	2.146	96.318	24209	1204	55.9	0.207	0.2036	0.2039	0.2684	0.2683	63.272

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]
0.011	0.005		0.011		-0.035

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.468
r_dihedral_angle_3_deg	16.839
r_dihedral_angle_6_deg	15.358
r_lrange_it	11.435
r_scangle_it	8.332
r_dihedral_angle_1_deg	7.51
r_mcangle_it	6.329
r_scbond_it	5.639
r_mcbond_it	4.04
r_angle_refined_deg	2.284
r_nbtor_refined	0.315
r_nbd_refined	0.24
r_symmetry_nbd_refined	0.227
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.134
r_symmetry_xyhbond_nbd_refined	0.104
r_bond_refined_d	0.011
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4629
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing