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Crystal structure of onconase double mutant with spontaneously-assembled (AMP) 4 stack
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 6.5 293 PROTEIN SOLUTION (21.4 MG/ML PROTEIN) MIXED
IN A 1:1 RATIO WITH THE
WELL SOLUTION (30.6% MEPEG 2K, 0.050 M AMP, 0.090 M BisTris pH 6.5) Crystals cryo-protected with the well solution
supplemented with 5% ethylene glycol, vapor diffusion, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.12 41.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.994 α = 90 b = 52.112 β = 90 c = 66.142 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 CCD BRUKER PROTEUM-R MONTEL OPTICS 2006-01-27 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 1.65 66.142 99.9 0.0542 40.66 26.59 12645
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) 1.65 1.7 99.6 0.6625 3.32 5.07 1046
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1onc 1.65 40.927 12597 612 99.889 0.168 0.1653 0.1665 0.2173 0.2182 RANDOM 19.346
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] -0.717 -0.534 1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.399 r_dihedral_angle_3_deg 12.735 r_dihedral_angle_1_deg 6.904 r_scangle_it 4.723 r_dihedral_angle_4_deg 3.664 r_scbond_it 3.193 r_mcangle_it 1.924 r_angle_refined_deg 1.718 r_mcbond_it 1.064 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.399 r_dihedral_angle_3_deg 12.735 r_dihedral_angle_1_deg 6.904 r_scangle_it 4.723 r_dihedral_angle_4_deg 3.664 r_scbond_it 3.193 r_mcangle_it 1.924 r_angle_refined_deg 1.718 r_mcbond_it 1.064 r_nbtor_refined 0.301 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.18 r_xyhbond_nbd_refined 0.124 r_symmetry_hbond_refined 0.114 r_chiral_restr 0.104 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 859 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 92
Software Software Software Name Purpose SAINT data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction