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Novel and retro Binding Modes in Cytotoxic Ribonucleases from Rana catesbeiana of Two Crystal Structures Complexed with d(ApCpGpA) and (2',5'CpG)
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 7 3.3 M AMMONIUM SULFATE,2% PEG 400, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.59 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.23 α = 90 b = 61.23 β = 90 c = 65.88 γ = 90
Symmetry Space Group P 43 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 IMAGE PLATE RIGAKU IMAGE PLATE CONFOCAL M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300
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 1.7 20 90.5 0.044 35.5 7.32 12965 2 20.7
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 1.7 1.76 97.5 0.43 4.8 7.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1ONC 1.7 20 2 11741 1218 82 0.229 0.229 0.2355 0.273 0.2778 RANDOM 29.6
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] 3.45 3.45 -6.9
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.7 c_scangle_it 3.23 c_scbond_it 2.19 c_mcangle_it 2.06 c_mcbond_it 1.45 c_angle_deg 1.4 c_improper_angle_d 0.91 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.7 c_scangle_it 3.23 c_scbond_it 2.19 c_mcangle_it 2.06 c_mcbond_it 1.45 c_angle_deg 1.4 c_improper_angle_d 0.91 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 849 Nucleic Acid Atoms 83 Solvent Atoms 220 Heterogen Atoms 10
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing