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Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in complex with 5-InsP7 in presence of Mg
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AUK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 291 25% PEG 3350, 0.1 M Sodium acetate pH 4.5, 0.1 M NaCl, 5 mM Magnesium chloride.
Protein buffer: 20 mM Tris pH 8.0, 150 mM NaCl, 1 mM DTT, 5 mM 5-InsP7.
Crystal Properties Matthews coefficient Solvent content 2.42 49.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.634 α = 90 b = 61.634 β = 90 c = 95.978 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M KB focusing mirrors 2020-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979260 ALBA XALOC
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.85 47.99 100 0.078 0.021 0.998 17.9 15.2 18607 32.802
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) Redundancy Number Unique Reflections (All) 1 1.85 1.89 100 0.65 0.183 0.914 3.2 13.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 7AUK 1.85 46.69 17636 938 99.98 0.2603 0.2591 0.2626 0.2814 0.2809 RANDOM 46.413
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] 0.08 0.04 0.08 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.263 r_dihedral_angle_3_deg 14.349 r_dihedral_angle_4_deg 12.902 r_dihedral_angle_1_deg 7.167 r_angle_refined_deg 1.414 r_angle_other_deg 1.135 r_chiral_restr 0.061 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.263 r_dihedral_angle_3_deg 14.349 r_dihedral_angle_4_deg 12.902 r_dihedral_angle_1_deg 7.167 r_angle_refined_deg 1.414 r_angle_other_deg 1.135 r_chiral_restr 0.061 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1367 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling REFMAC phasing Coot model building