7OG1 | pdb_00007og1

AP2 clathrin adaptor core in complex with cargo peptide and FCHO2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XA7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289	Crystals of AP-2 in complex with FCHO2 linker and TGN38 peptide, supplemented with 10mM K Na Tartrate, grew in sitting drops with reservoir 0.1M Mg formate dehydrate, 10% to 15% PEG 3350. The crystals were cryo-protected with 0.1M Mg formate dehydrate, 13% PEG 3350, 18-24% Glycerol and 1mg/ml of peptide.

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.576	α = 90
b = 150.07	β = 112.652
c = 96.43	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 PILATUS3 6M		2017-04-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.92001	Diamond	I04

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	3.25	78.58	100	0.133	0.159	0.086	0.998	7.2	6.6		38355

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	3.25	3.39	100		2.123	2.59	1.465	0.366	0.8	6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	2xa7	3.25	76.662	38326	1881	99.924	0.212	0.2066	0.21	0.3063	0.3	135.397

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]
-2.812		3.095	-4.448		3.469

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.559
r_lrange_it	23.935
r_lrange_other	23.935
r_dihedral_angle_3_deg	22.635
r_mcangle_it	18.686
r_mcangle_other	18.685
r_scangle_it	17.117
r_scangle_other	17.116
r_dihedral_angle_4_deg	15.69
r_mcbond_it	12.128
r_mcbond_other	12.126
r_scbond_it	10.82
r_scbond_other	10.819
r_dihedral_angle_1_deg	9.291
r_angle_refined_deg	1.578
r_angle_other_deg	1.115
r_symmetry_nbd_refined	0.261
r_nbd_refined	0.241
r_nbd_other	0.206
r_symmetry_nbd_other	0.199
r_xyhbond_nbd_refined	0.196
r_nbtor_refined	0.171
r_symmetry_nbtor_other	0.079
r_symmetry_xyhbond_nbd_other	0.071
r_chiral_restr	0.061
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_symmetry_xyhbond_nbd_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14392
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PHASER	phasing
PHENIX	refinement
Aimless	data scaling
DIALS	data reduction