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The crystal structure of the domain-swapped dimer of onconase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ONC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 20% PEG 3350
0.2 M sodium citrate tribasic
Crystal Properties Matthews coefficient Solvent content 31.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.29 α = 90 b = 60.05 β = 90 c = 101.78 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 PILATUS 6M 2020-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.9999 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 2.12 51.72 99.9 0.273 1 9.1 12.2 10440
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 2.12 2.15 100 0.7 2.2
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-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1ONC 2.12 51.719 9681 499 92.863 0.188 0.1855 0.2432 0.2194 24.241
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] 0.111 -0.162 0.051
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.901 r_dihedral_angle_4_deg 26.743 r_dihedral_angle_3_deg 18.536 r_dihedral_angle_1_deg 8.978 r_lrange_it 5.955 r_lrange_other 5.905 r_scangle_it 3.967 r_scangle_other 3.966 r_mcangle_other 3.023 r_mcangle_it 3.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.901 r_dihedral_angle_4_deg 26.743 r_dihedral_angle_3_deg 18.536 r_dihedral_angle_1_deg 8.978 r_lrange_it 5.955 r_lrange_other 5.905 r_scangle_it 3.967 r_scangle_other 3.966 r_mcangle_other 3.023 r_mcangle_it 3.015 r_scbond_it 2.515 r_scbond_other 2.511 r_mcbond_it 1.82 r_mcbond_other 1.791 r_angle_refined_deg 1.564 r_angle_other_deg 1.278 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.196 r_symmetry_nbd_other 0.19 r_nbd_other 0.173 r_nbtor_refined 0.165 r_symmetry_nbd_refined 0.154 r_symmetry_xyhbond_nbd_refined 0.144 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.066 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1652 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing