6D7O

Crystal Structure of Rat TRPV6* in complex with 2-Aminoethoxydiphenyl borate (2-APB)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5WO7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION829320-24% PEG 350 MME, 50 mM NaCl, and 50 mM Tris-HCl pH 8.0-8.5
Crystal Properties
Matthews coefficientSolvent content
469.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 145.384α = 90
b = 145.384β = 90
c = 116.162γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-09-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.9791APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.45094.920.13111.448.5166421.02
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.43.693.31.4096.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5WO73.4547.0051.351635081796.490.28620.28460.3156
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.251
f_angle_d0.588
f_chiral_restr0.037
f_plane_restr0.004
f_bond_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4725
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms33

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
HKL-2000data scaling
PHASERphasing