9F8T | pdb_00009f8t

Clathrin terminal domain complexed with C-terminus of AAK1L

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1UTC	1UTC_1 (chain A/B)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293.15	20% PEG 3,350; 100 mM Bis-Tris propane, pH 6.0; 200 mM sodium citrate; 10 mM DTT

Crystal Properties
Matthews coefficient	Solvent content
3.24	62.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.539	α = 90
b = 130.86	β = 90
c = 77.05	γ = 90

Symmetry
Space Group	C 2 2 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	PIXEL	DECTRIS PILATUS 6M		2016-01-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.71	28.3	95.47	0.0686	0.097	0.0686	0.987	4.83	1.87		56178

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.71	1.77	88.8		0.452	0.64	0.452	0.603	1.15	1.83

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	1.711	28.264	56177	2770	95.473	0.174	0.1723	0.1815	0.2092	0.2182	24.229

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]
0.466			0.588		-1.054

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.734
r_dihedral_angle_3_deg	12.247
r_dihedral_angle_2_deg	12.123
r_lrange_it	8.051
r_lrange_other	7.84
r_dihedral_angle_1_deg	7.238
r_scangle_it	5.962
r_scangle_other	5.961
r_mcangle_other	3.843
r_mcangle_it	3.837
r_scbond_it	3.805
r_scbond_other	3.804
r_mcbond_it	2.538
r_mcbond_other	2.529
r_angle_refined_deg	1.677
r_angle_other_deg	0.906
r_symmetry_xyhbond_nbd_refined	0.254
r_symmetry_nbd_other	0.213
r_nbd_refined	0.199
r_nbd_other	0.179
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.174
r_symmetry_nbd_refined	0.169
r_symmetry_nbtor_other	0.093
r_chiral_restr	0.087
r_gen_planes_other	0.011
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2933
Nucleic Acid Atoms
Solvent Atoms	384
Heterogen Atoms

Software

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