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Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilament arrangement, bound to 53% GTP/47% and 2 Na+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7EVC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 25% PEG 1500, 0.1 M MMT (1 DL-malic acid: 2 MES: 2 Tris base), pH 9.0, soaked with 10 mM GTP for 2 h, before back soaking without GTP (70 h), before freezing
Crystal Properties Matthews coefficient Solvent content 2.01 38.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.361 α = 90 b = 92.104 β = 90 c = 102.824 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-300 2020-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 1.0 NSRRC TPS 05A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.45 20 98.8 0.114 0.119 0.035 34.2 10.9 67867
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 1.45 1.47 0.593 0.723 0.387 0.554 1
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7evc 1.45 19.9 67742 5906 98.4 0.152 0.152 0.1762 0.1762 20.7
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 20.7206 f_angle_d 1.5348 f_chiral_restr 0.1161 f_bond_d 0.0154 f_plane_restr 0.0097
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3326 Nucleic Acid Atoms Solvent Atoms 379 Heterogen Atoms 62
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing