7AUQ

Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in complex with Ap5A and Ca2+


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP529127% PEG 1500, 0.1 M PCB pH 5.0, 5 mM Calcium chloride. Protein buffer: 20 mM Tris pH 8.0, 150 mM NaCl, 1 mM DTT, 10 mM Ap5A.
Crystal Properties
Matthews coefficientSolvent content
2.4349.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.999α = 90
b = 61.999β = 90
c = 95.405γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKB focusing mirrors2019-10-19MSINGLE 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
12.2546.8497.90.1050.0350.99511.79.61018455.09
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)
12.252.3299.50.6520.2110.8833.310

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 SYNTHESISTHROUGHOUT7AUI2.2546.84970347996.760.20620.20520.2284RANDOM63.829
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]
-1.18-0.59-1.183.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.425
r_dihedral_angle_3_deg18.396
r_dihedral_angle_4_deg17.789
r_dihedral_angle_1_deg6.427
r_angle_refined_deg1.639
r_angle_other_deg1.271
r_chiral_restr0.071
r_bond_refined_d0.008
r_bond_other_d0.006
r_gen_planes_refined0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.425
r_dihedral_angle_3_deg18.396
r_dihedral_angle_4_deg17.789
r_dihedral_angle_1_deg6.427
r_angle_refined_deg1.639
r_angle_other_deg1.271
r_chiral_restr0.071
r_bond_refined_d0.008
r_bond_other_d0.006
r_gen_planes_refined0.006
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1144
Nucleic Acid Atoms
Solvent Atoms37
Heterogen Atoms50

Software

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