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Crystal structure of the polymerising VEL domain of VIN3 (I575D mutant)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 1M potassium phosphate monobasic, 3 % v/v 2 propanol, 0.1M sodium cacodylate pH6.5
Crystal Properties Matthews coefficient Solvent content 2 38.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.498 α = 90 b = 91.273 β = 90 c = 98.413 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 2020-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04
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 2.4 29.07 100 1 13.3 8.7 11740
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 2.4 2.49 0.91
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.4 29.07 11697 590 99.923 0.226 0.2234 0.2262 0.2695 0.2652 56.228
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] 7.125 -4.445 -2.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.297 r_dihedral_angle_4_deg 25.54 r_dihedral_angle_3_deg 19.017 r_lrange_it 11.503 r_lrange_other 11.502 r_scangle_it 9.224 r_scangle_other 9.222 r_mcangle_it 6.32 r_mcangle_other 6.318 r_scbond_it 5.883
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.297 r_dihedral_angle_4_deg 25.54 r_dihedral_angle_3_deg 19.017 r_lrange_it 11.503 r_lrange_other 11.502 r_scangle_it 9.224 r_scangle_other 9.222 r_mcangle_it 6.32 r_mcangle_other 6.318 r_scbond_it 5.883 r_scbond_other 5.88 r_dihedral_angle_1_deg 5.543 r_mcbond_other 4.364 r_mcbond_it 4.363 r_angle_refined_deg 1.532 r_angle_other_deg 1.314 r_symmetry_xyhbond_nbd_refined 0.374 r_symmetry_nbd_refined 0.238 r_nbd_refined 0.216 r_symmetry_nbd_other 0.203 r_xyhbond_nbd_refined 0.19 r_nbd_other 0.177 r_nbtor_refined 0.171 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.076 r_xyhbond_nbd_other 0.072 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2319 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling CRANK2 phasing Coot model building PDB_EXTRACT data extraction