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Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilament arrangement, bound 78% GTP/22% GDP 1 K+, 1 Mg2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7EVB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 25% PEG 1500
0.1 M MMT (1 DL-malic acid: 2 MES: 2 Tris base), pH 9.0
Soak: 10 mM GTP, 1 mM MgCl2, 100 mM KCl (1 h)
Crystal Properties Matthews coefficient Solvent content 2.02 39.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.416 α = 90 b = 92.835 β = 90 c = 102.516 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 PIXEL DECTRIS EIGER2 X 16M 2021-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
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 1.9 29.62 100 0.123 0.127 0.028 14.9 19.9 31257
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 1.9 1.94 100 2.337 2.397 0.529 0.75 1.7 20.3
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 7EVB 1.9 29.2 31181 1630 99.9 0.1795 0.1804 0.2204 0.2199 38.92
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 20.7813 f_angle_d 1.143 f_chiral_restr 0.0678 f_bond_d 0.0115 f_plane_restr 0.0072
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3334 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 62
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing