7AUP

Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in complex with PCP-InsP7


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7AUN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.529120% PEG 3350, 0.1 M Sodium acetate pH 4.5, 0.1 M NaCl. Protein buffer: 20 mM Tris pH 8.0, 150 mM NaCl, 1 mM DTT, 10 mM PCP-InsP7.
Crystal Properties
Matthews coefficientSolvent content
2.4249.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.702α = 90
b = 61.702β = 90
c = 95.844γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKB focusing mirrors2019-04-27MSINGLE 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
11.8546.721000.0520.013133.218.61862532.47
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)
11.851.891000.6520.160.9156.217.9

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT7AUN1.8546.721765693699.940.22580.22340.2682RANDOM46.945
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]
0.20.10.2-0.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.786
r_dihedral_angle_3_deg15.78
r_dihedral_angle_4_deg15.437
r_dihedral_angle_1_deg7.45
r_angle_refined_deg1.826
r_angle_other_deg1.322
r_chiral_restr0.085
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.786
r_dihedral_angle_3_deg15.78
r_dihedral_angle_4_deg15.437
r_dihedral_angle_1_deg7.45
r_angle_refined_deg1.826
r_angle_other_deg1.322
r_chiral_restr0.085
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1294
Nucleic Acid Atoms
Solvent Atoms68
Heterogen Atoms82

Software

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