3KYQ | pdb_00003kyq

Lipid-induced Conformational Switch Controls Fusion Activity of Longin Domain SNARE Ykt6

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BW6	PDB ENTRY 3BW6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	289	2M (NH4)2SO4, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.81	α = 90
b = 59.71	β = 90
c = 108.33	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV++		2008-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	2.443	30	100	0.067	10	5.1	6900	6788

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	2.443	2.506	100		0.336	2.2	5.2

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 3BW6	2.443	30	6195	683	99.96	0.20516	0.1994	0.2	0.26137	0.26	RANDOM	33.673

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]
-0.49			1.11		-0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.731
r_dihedral_angle_3_deg	17.486
r_dihedral_angle_4_deg	14.732
r_dihedral_angle_1_deg	5.369
r_scangle_it	1.581
r_angle_refined_deg	1.06
r_scbond_it	0.98
r_mcangle_it	0.936
r_mcbond_it	0.605
r_nbtor_refined	0.297

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.731
r_dihedral_angle_3_deg	17.486
r_dihedral_angle_4_deg	14.732
r_dihedral_angle_1_deg	5.369
r_scangle_it	1.581
r_angle_refined_deg	1.06
r_scbond_it	0.98
r_mcangle_it	0.936
r_mcbond_it	0.605
r_nbtor_refined	0.297
r_symmetry_vdw_refined	0.222
r_nbd_refined	0.187
r_xyhbond_nbd_refined	0.145
r_symmetry_hbond_refined	0.105
r_chiral_restr	0.074
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1540
Nucleic Acid Atoms
Solvent Atoms	86
Heterogen Atoms	33

Software

Software
Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	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 R01GM157729.