7AUR

Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in complex with AMP-PNP


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP529125% PEG 6000, 0.1 M Sodium acetate pH 5.0, 0.1 M NaCl. Protein:precipitant ratio 2:1. Protein buffer: 20 mM Tris pH 8.0, 150 mM NaCl, 1 mM DTT, 10 mM AMP-PNP.
Crystal Properties
Matthews coefficientSolvent content
2.4449.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.958α = 90
b = 61.958β = 90
c = 95.924γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKB focusing mirrors2018-12-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979300ALBAXALOC

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
11.6547.9699.80.0830.020.99918.9192624027.77
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)
11.651.6899.80.6660.1640.9374.817.2

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 REPLACEMENTTHROUGHOUT7AUI1.6546.8724867133699.80.21060.2090.242RANDOM35.977
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]
0.140.070.14-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.579
r_dihedral_angle_3_deg13.725
r_dihedral_angle_4_deg10.445
r_dihedral_angle_1_deg6.796
r_angle_refined_deg1.512
r_angle_other_deg1.301
r_chiral_restr0.071
r_bond_refined_d0.007
r_bond_other_d0.007
r_gen_planes_refined0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.579
r_dihedral_angle_3_deg13.725
r_dihedral_angle_4_deg10.445
r_dihedral_angle_1_deg6.796
r_angle_refined_deg1.512
r_angle_other_deg1.301
r_chiral_restr0.071
r_bond_refined_d0.007
r_bond_other_d0.007
r_gen_planes_refined0.007
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1158
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms96

Software

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