7AUJ

Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 mutation E80Q in complex with 1-InsP7


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.529115% 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, 2 mM 1-InsP7.
Crystal Properties
Matthews coefficientSolvent content
2.4549.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.893α = 90
b = 61.893β = 90
c = 96.513γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKB focusing mirrors2020-01-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979257ALBAXALOC

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
12.148.261000.0530.0150.99926.113.11300243.232
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)
12.12.1699.90.5580.1570.964.813.6

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 SYNTHESISTHROUGHOUT7AUI2.146.91231263299.680.22740.22540.2654RANDOM59.787
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]
-0.22-0.11-0.220.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.75
r_dihedral_angle_3_deg17.678
r_dihedral_angle_4_deg12.977
r_dihedral_angle_1_deg6.33
r_angle_refined_deg1.281
r_angle_other_deg1.101
r_chiral_restr0.05
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.75
r_dihedral_angle_3_deg17.678
r_dihedral_angle_4_deg12.977
r_dihedral_angle_1_deg6.33
r_angle_refined_deg1.281
r_angle_other_deg1.101
r_chiral_restr0.05
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1279
Nucleic Acid Atoms
Solvent Atoms38
Heterogen Atoms41

Software

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