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Crystal structure of the 5-phosphatase domain of Synaptojanin1 bound to its substrate diC8-PI(3,4,5)P3 in complex with a nanobody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I9Y 1i9y, 3n9v, 3mtc, 4cmn, 4nc2 experimental model PDB 3N9V 1i9y, 3n9v, 3mtc, 4cmn, 4nc2 experimental model PDB 3MTC 1i9y, 3n9v, 3mtc, 4cmn, 4nc2 experimental model PDB 4CMN 1i9y, 3n9v, 3mtc, 4cmn, 4nc2 experimental model PDB 4NC2 1i9y, 3n9v, 3mtc, 4cmn, 4nc2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 15% PEG 3350, 0.1 M sodium citrate pH 5.5, 13% ethanol
Crystal Properties Matthews coefficient Solvent content 2.42 49.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.323 α = 90 b = 109.205 β = 120.62 c = 100.902 γ = 90
Symmetry Space Group C 1 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 EIGER X 9M 2019-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.976246 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.728 87.39 91.5 0.2 0.282 0.148 0.97 5.3 3.5 32151 43.28
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.728 3.02 0.474 1.4 3.6
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 MOLECULAR REPLACEMENT THROUGHOUT 1i9y, 3n9v, 3mtc, 4cmn, 4nc2 2.73 87.39 30520 1630 76.22 0.19881 0.19578 0.2027 0.25744 0.2617 RANDOM 43.603
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] 0.45 -0.41 0.37 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.129 r_dihedral_angle_4_deg 16.634 r_dihedral_angle_3_deg 15.703 r_long_range_B_refined 8.871 r_long_range_B_other 8.871 r_mcangle_it 6.054 r_mcangle_other 6.054 r_scangle_other 5.789 r_dihedral_angle_1_deg 5.754 r_mcbond_it 3.752
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.129 r_dihedral_angle_4_deg 16.634 r_dihedral_angle_3_deg 15.703 r_long_range_B_refined 8.871 r_long_range_B_other 8.871 r_mcangle_it 6.054 r_mcangle_other 6.054 r_scangle_other 5.789 r_dihedral_angle_1_deg 5.754 r_mcbond_it 3.752 r_mcbond_other 3.751 r_scbond_it 3.632 r_scbond_other 3.632 r_angle_refined_deg 1.079 r_angle_other_deg 0.934 r_chiral_restr 0.066 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10616 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building