5F0P | pdb_00005f0p

Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1(L557M) (SeMet labeled)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5F0L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	291	0.8 M AmSO4, 0.1 M MES pH 6.0, 10% Glycerol

Crystal Properties
Matthews coefficient	Solvent content
3.52	65.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 371.29	α = 90
b = 75.32	β = 97.66
c = 57.27	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	PIXEL	DECTRIS PILATUS 6M		2015-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.97895	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	2.77	56.761	99.1	0.066	0.078	0.999	12.17			77507		-3	80.168

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.77	2.94	95.3		0.904	1.073	0.808	1.33

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	5F0L	2.78	56.76	36032	1901	95.13	0.2209	0.2189	0.22	0.2605	0.26	RANDOM	70.57

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]
-0.04		-0.73	0.09		0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.632
r_dihedral_angle_4_deg	14.651
r_dihedral_angle_3_deg	13.526
r_dihedral_angle_1_deg	5.79
r_mcangle_it	4.414
r_mcbond_it	2.512
r_mcbond_other	2.512
r_angle_refined_deg	1.135
r_angle_other_deg	0.851
r_chiral_restr	0.064

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.632
r_dihedral_angle_4_deg	14.651
r_dihedral_angle_3_deg	13.526
r_dihedral_angle_1_deg	5.79
r_mcangle_it	4.414
r_mcbond_it	2.512
r_mcbond_other	2.512
r_angle_refined_deg	1.135
r_angle_other_deg	0.851
r_chiral_restr	0.064
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7453
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	135

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

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.