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Crystal structure of the polymerising VEL domain of VIN3 (R556D I575D mutant)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.06M Morpheus Divalents, 0.1M Morpheus Buffer System 2 pH 7.5, 10% w/v PEG 8K, 20% v/v
ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.06 40.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.423 α = 90 b = 51.809 β = 90 c = 85.01 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 2.02 29.49 99.7 1 36.2 20 9677
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 2.02 2.07 0.93
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.02 29.49 9131 506 99.71 0.20241 0.2139 0.23655 0.2598 RANDOM 49.648
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] -1.23 3.04 -1.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.351 r_dihedral_angle_4_deg 19.995 r_dihedral_angle_3_deg 12.934 r_long_range_B_other 7.851 r_long_range_B_refined 7.845 r_scangle_other 6.328 r_scbond_it 4.05 r_scbond_other 4.049 r_dihedral_angle_1_deg 3.993 r_mcangle_it 3.557
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.351 r_dihedral_angle_4_deg 19.995 r_dihedral_angle_3_deg 12.934 r_long_range_B_other 7.851 r_long_range_B_refined 7.845 r_scangle_other 6.328 r_scbond_it 4.05 r_scbond_other 4.049 r_dihedral_angle_1_deg 3.993 r_mcangle_it 3.557 r_mcangle_other 3.555 r_mcbond_other 2.731 r_mcbond_it 2.729 r_angle_refined_deg 1.228 r_angle_other_deg 1.099 r_chiral_restr 0.063 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1173 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling CRANK2 phasing Coot model building PDB_EXTRACT data extraction