☰ Navigation Tabs
Crystal structure of onconase with bound nucleic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ONC PDB ENTRY 1ONC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.003 M SINGLE-STRANDED DNA OLIGOMER) MIXED IN A 1:1 RATIO WITH WELL SOLUTION (25% PEG 3350, 0.1 M HEPES PH 7.5) CRYO-PROTECTED WITH WELL SOLUTION SUPPLEMENTED WITH 20% ETHYLENE GLYCOL, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.9 41.186596
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.229 α = 90 b = 26.101 β = 90 c = 32.486 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD BRUKER SMART 6000 MONTEL OPTICS 2006-05-02 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 64.6145 99.7 0.1249 12.3 9.84 9270
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 1.95 95.9 0.5172 2.52 3.32 624
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-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT PDB ENTRY 1ONC 1.9 32.49 9229 441 99.719 0.181 0.181 0.178 0.177 0.24 0.2458 RANDOM 16.602
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] -0.207 -0.009 0.216
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.533 r_dihedral_angle_4_deg 20.535 r_dihedral_angle_3_deg 14.183 r_dihedral_angle_1_deg 6.706 r_scangle_it 5.99 r_scbond_it 4.173 r_mcangle_it 2.209 r_angle_refined_deg 1.415 r_mcbond_it 1.361 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.533 r_dihedral_angle_4_deg 20.535 r_dihedral_angle_3_deg 14.183 r_dihedral_angle_1_deg 6.706 r_scangle_it 5.99 r_scbond_it 4.173 r_mcangle_it 2.209 r_angle_refined_deg 1.415 r_mcbond_it 1.361 r_nbtor_refined 0.303 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.15 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.098 r_symmetry_hbond_refined 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 826 Nucleic Acid Atoms 41 Solvent Atoms 155 Heterogen Atoms
Software Software Software Name Purpose SAINT data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction SAINT data reduction