Experiment: 4GSL

Crystal structure of an Atg7-Atg3 crosslinked complex

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3T7E	PDB ENTRIES 3T7E, 3T7F, AND 2DYT
experimental model	PDB	3T7F	PDB ENTRIES 3T7E, 3T7F, AND 2DYT
experimental model	PDB	2DYT	PDB ENTRIES 3T7E, 3T7F, AND 2DYT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.8	294	100 mM sodium citrate, pH 5.8, 13.5% PEG4000, 10% isopropanol, 5% dioxane, 88 mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 281.556	α = 90
b = 125.083	β = 103.32
c = 71.079	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 QUANTUM 315		2012-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.9792	APS	24-ID-E

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	2.7	40	99.5	0.079	17.8	4.1	65155	64845

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	2.7	2.8	99		0.556		4	6400

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	PDB ENTRIES 3T7E, 3T7F, AND 2DYT	2.703	37.073	64763	64763	1901	98.66	0.1943	0.1943	0.1927	0.1875	0.2462	0.2432	RANDOM	70.5395

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]
6.8972		-4.4035	-6.0097		-0.8876

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.171
f_angle_d	1.214
f_chiral_restr	0.081
f_bond_d	0.009
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12498
Nucleic Acid Atoms
Solvent Atoms	43
Heterogen Atoms	2

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing