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Crystal structure of the VIN3 VEL polymerising domain (R554A R556D mutant)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 15% v/v ethanol, 0.1M citrate pH 5.5, 0.2M lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.13 42.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.758 α = 90 b = 40.758 β = 90 c = 83.966 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 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 1.84 28.84 99.7 1 39.2 13.8 5941
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 1.84 1.88 0.906
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 (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 1.84 28.84 5348 566 99.56 0.22364 0.22129 0.2298 0.24438 0.2513 RANDOM 47.917
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] 0.88 0.88 -1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.291 r_dihedral_angle_3_deg 13.989 r_dihedral_angle_4_deg 13.48 r_long_range_B_refined 6.216 r_long_range_B_other 6.207 r_scangle_other 5.308 r_dihedral_angle_1_deg 5.096 r_scbond_it 3.733 r_scbond_other 3.703 r_mcangle_it 3.232
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.291 r_dihedral_angle_3_deg 13.989 r_dihedral_angle_4_deg 13.48 r_long_range_B_refined 6.216 r_long_range_B_other 6.207 r_scangle_other 5.308 r_dihedral_angle_1_deg 5.096 r_scbond_it 3.733 r_scbond_other 3.703 r_mcangle_it 3.232 r_mcangle_other 3.229 r_mcbond_other 2.614 r_mcbond_it 2.609 r_angle_refined_deg 1.507 r_angle_other_deg 1.192 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_bond_other_d 0.004 r_gen_planes_refined 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 572 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling CRANK2 phasing Coot model building PDB_EXTRACT data extraction