3F6K

Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with neurotensin

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.8	293	19% PEG 6000, 600 mM NaCl, 3% Glycerol, 100 mM HEPES, 93 mM Tris-HCl, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 145.76	α = 90
b = 74.53	β = 131.87
c = 108.33	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	MARMOSAIC 225 mm CCD		2005-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.95008	SLS	X06SA

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	50	96.9	0.073	11.59	3.6	58793	56985		-3	37.05

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	2.1	98.8		0.44	4.32	3.7	7942

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MIRAS	THROUGHOUT	2	40.32	56985	56985	2904	97.39	0.20524	0.20524	0.20395	0.22879	RANDOM	31.78

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]
-0.58		-0.78	1.22		-1.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.684
r_dihedral_angle_4_deg	22.079
r_dihedral_angle_3_deg	16.77
r_dihedral_angle_1_deg	7.053
r_scangle_it	4.816
r_scbond_it	3.273
r_mcangle_it	2.29
r_angle_refined_deg	1.832
r_mcbond_it	1.446
r_nbtor_refined	0.319

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.684
r_dihedral_angle_4_deg	22.079
r_dihedral_angle_3_deg	16.77
r_dihedral_angle_1_deg	7.053
r_scangle_it	4.816
r_scbond_it	3.273
r_mcangle_it	2.29
r_angle_refined_deg	1.832
r_mcbond_it	1.446
r_nbtor_refined	0.319
r_xyhbond_nbd_refined	0.268
r_nbd_refined	0.238
r_symmetry_hbond_refined	0.235
r_symmetry_vdw_refined	0.223
r_chiral_restr	0.137
r_bond_refined_d	0.021
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5212
Nucleic Acid Atoms
Solvent Atoms	305
Heterogen Atoms	83

Software

Software
Software Name	Purpose
XDS	data scaling
SHARP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

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 R01GM133198.