3L81 | pdb_00003l81

Crystal structure of adaptor protein complex 4 (AP-4) mu4 subunit C-terminal domain, in complex with a sorting peptide from the amyloid precursor protein (APP)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295	10% PEG 3350, 10mM magnesium chloride, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
2	VAPOR DIFFUSION, HANGING DROP	7	295	15% PEG 6000, 3% trimethylamine N-oxide dihydrate, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.672	α = 90
b = 56.91	β = 106.53
c = 60.664	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	CCD	MARMOSAIC 300 mm CCD		2009-03-20	M	MAD
2	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD		2009-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.9794, 0.9796, 0.9719	APS	23-ID-D
2	SYNCHROTRON	APS BEAMLINE 22-ID	1.0000	APS	22-ID

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
1,2	1.6	50	97.3	0.097	13.8	4.4	39566	39268		1.48

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.6	41.67	39268	1972	97.47	0.209	0.207	0.2	0.252	0.25	RANDOM	27.823

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]
		0.01	0.01		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.233
r_dihedral_angle_4_deg	22.493
r_dihedral_angle_3_deg	14.962
r_dihedral_angle_1_deg	7.632
r_scangle_it	4.817
r_scbond_it	3.087
r_mcangle_it	2.36
r_angle_refined_deg	1.731
r_mcbond_it	1.474
r_nbtor_refined	0.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.233
r_dihedral_angle_4_deg	22.493
r_dihedral_angle_3_deg	14.962
r_dihedral_angle_1_deg	7.632
r_scangle_it	4.817
r_scbond_it	3.087
r_mcangle_it	2.36
r_angle_refined_deg	1.731
r_mcbond_it	1.474
r_nbtor_refined	0.312
r_symmetry_vdw_refined	0.249
r_symmetry_hbond_refined	0.22
r_nbd_refined	0.212
r_xyhbond_nbd_refined	0.169
r_chiral_restr	0.125
r_bond_refined_d	0.015
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2038
Nucleic Acid Atoms
Solvent Atoms	153
Heterogen Atoms	18

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.