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The crystal structure of the domain-swapped dimer of onconase (2)
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 8.5 298 0.1 M Tris-HCl pH 8.5
25% PEG 3350
0.2 M Ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.15 42.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.75 α = 90 b = 28.54 β = 94.24 c = 61.48 γ = 90
Symmetry Space Group P 1 21 1
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 1 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 2.14 58.59 97.4 0.124 1 10.6 5.9 11313
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 2.14 2.18 0.6 2.3 4.3
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-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1ONC 2.14 58.59 10936 526 94.081 0.214 0.2118 0.2668 0.2486 29.169
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] -0.428 0.077 -0.043 0.455
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.359 r_dihedral_angle_4_deg 22.241 r_dihedral_angle_3_deg 17.051 r_lrange_it 8.414 r_dihedral_angle_1_deg 8.353 r_lrange_other 8.305 r_scangle_it 5.132 r_scangle_other 5.128 r_mcangle_it 3.996 r_mcangle_other 3.994
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.359 r_dihedral_angle_4_deg 22.241 r_dihedral_angle_3_deg 17.051 r_lrange_it 8.414 r_dihedral_angle_1_deg 8.353 r_lrange_other 8.305 r_scangle_it 5.132 r_scangle_other 5.128 r_mcangle_it 3.996 r_mcangle_other 3.994 r_scbond_it 3.248 r_scbond_other 3.231 r_mcbond_other 2.475 r_mcbond_it 2.474 r_angle_refined_deg 1.636 r_angle_other_deg 1.235 r_nbd_other 0.248 r_symmetry_nbd_refined 0.244 r_xyhbond_nbd_refined 0.224 r_nbd_refined 0.204 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.164 r_symmetry_xyhbond_nbd_refined 0.16 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.065 r_symmetry_xyhbond_nbd_other 0.051 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 97 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing