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Crystal structure of the 5-phosphatase domain of Synaptojanin1 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 5 293 15% PEG 4000, 0.1 M sodium citrate pH 5, 10% 2-propanol
Crystal Properties Matthews coefficient Solvent content 2.61 52.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.874 α = 90 b = 108.793 β = 120.718 c = 100.974 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 EIGER2 XE 16M 2019-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.980105 Diamond I03
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 2.297 86.81 92.3 0.133 0.143 0.054 0.997 11.2 7 53823 38.08
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 2.3 2.43 0.512
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1i9y, 3n9v, 3mtc, 4cmn, 4nc2 2.3 86.81 1.34 53805 2764 76.86 0.1992 0.1964 0.1964 0.2523 0.2526 47.27
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 21.9765 f_angle_d 0.48 f_chiral_restr 0.321 f_plane_restr 0.0033 f_bond_d 0.0019
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10536 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 42
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing