7AUI

Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in complex with InsP6


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FVV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.529125% PEG 6000, 0.1 M Sodium acetate pH 4.5, 0.1 M NaCl. Protein:precipitant ratio 2:1. Protein buffer: 20 mM Tris pH 8.0, 150 mM NaCl, 1 mM DTT, 5 mM InsP6.
Crystal Properties
Matthews coefficientSolvent content
2.4449.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.776α = 90
b = 61.776β = 90
c = 96.458γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6MKB focusing mirrors2018-11-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979260ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim 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
11.9848.231000.050.013132.317.31538536.149
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.982.031000.6630.1590.925.518.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2FVV1.9846.831457777999.980.20830.20760.2206RANDOM46.076
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]
0.220.110.22-0.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.014
r_dihedral_angle_3_deg15.57
r_dihedral_angle_4_deg14.571
r_dihedral_angle_1_deg7.258
r_angle_refined_deg1.546
r_angle_other_deg1.232
r_chiral_restr0.061
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.014
r_dihedral_angle_3_deg15.57
r_dihedral_angle_4_deg14.571
r_dihedral_angle_1_deg7.258
r_angle_refined_deg1.546
r_angle_other_deg1.232
r_chiral_restr0.061
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1286
Nucleic Acid Atoms
Solvent Atoms76
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
Cootmodel building