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Crystal structure of Triosephosphate Isomerase from Schizosaccharomyces pombe (SpTIM wt)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FF7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 293.15 2.2 M Ammonium sulphate, 0.2 M Lithium acetate, 9.1 mg/mL protein concentration
Crystal Properties Matthews coefficient Solvent content 2.5 50.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.51 α = 90 b = 149.51 β = 90 c = 99.91 γ = 90
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 2M 2021-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
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 1.79 37.38 99.77 0.09633 0.1035 0.03754 0.999 13.11 7.6 103063 36.36
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.79 1.854 98.26 1.437 0.915 0.9385 0.307 0.99 7.6
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 4FF7 1.79 37.38 1.33 103029 2100 99.79 0.1825 0.1817 0.1826 0.2179 0.2183 40.25
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 7.1038 f_angle_d 1.3065 f_chiral_restr 0.0835 f_bond_d 0.0151 f_plane_restr 0.0105
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7366 Nucleic Acid Atoms Solvent Atoms 855 Heterogen Atoms 46
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing