2VJ0 | pdb_00002vj0

Crystal structure of the alpha-adaptin appendage domain, from the AP2 adaptor complex, in complex with an FXDNF peptide from amphiphysin1 and a WVXF peptide from synaptojanin P170

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1B9K	PDB ENTRY 1B9K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		1.2M AMMONIUM SULPHATE, 3% ISOPROPANOL AND 0.05M SODIUM CITRATE PH 6.5

Crystal Properties
Matthews coefficient	Solvent content
3.2	61.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.508	α = 90
b = 66.98	β = 94.92
c = 39.73	γ = 90

Symmetry
Space Group	C 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	CCD	ADSC CCD	BENT MIRRORS	2004-02-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX9.6		SRS	PX9.6

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.6	17.76	96.3	0.08	10.8	2.7		47896		2	17.59

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.69	89.2		0.37	2	2.4

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1B9K	1.6	17.76	47892	2427	96.2	0.182	0.181	0.19	0.208	0.22	RANDOM	16.14

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]
0.205		0.164	-0.34		0.164

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.269
r_dihedral_angle_4_deg	16.453
r_dihedral_angle_3_deg	11.206
r_dihedral_angle_1_deg	6.099
r_scangle_it	3.362
r_scbond_it	2.197
r_mcangle_it	1.426
r_angle_refined_deg	1.299
r_mcbond_it	1.001
r_nbd_refined	0.202
r_symmetry_vdw_refined	0.18
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.151
r_symmetry_hbond_refined	0.126
r_chiral_restr	0.078
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2068
Nucleic Acid Atoms
Solvent Atoms	343
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing