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Crystal structure of Vaspin with PolyP45
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IF8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 0.1 M ammonium sulfate, 0.1 M sodium citrate, pH 5.1, 9% (w/v) PEG 4000, 5% (v/v) DMSO, 0.5% (w/v) n-Octyl-beta-D-glucoside
Crystal Properties Matthews coefficient Solvent content 3.36 63.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.257 α = 90 b = 147.977 β = 104.95 c = 62.464 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 PILATUS 6M 2023-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9762 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.26 101.08 91.2 0.998 11.4 7 40630
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 2.26 2.48 0.569
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.26 35.37 1.35 40596 2059 69.16 0.2189 0.2178 0.2255 0.2404 0.2455
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 13.315 f_angle_d 0.518 f_chiral_restr 0.043 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6007 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 54
Software Software Software Name Purpose STARANISO data scaling XDS data reduction PHASER phasing REFMAC refinement Coot model building PHENIX refinement