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Crystal structure of a new ribosome-inactivating protein (RIP): dianthin 30
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QI7 PBD ENTRY 1QI7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.5 293 PEG 4000, ammonium acetate, sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 4.50
Crystal Properties Matthews coefficient Solvent content 1.72 28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.568 α = 90 b = 78.654 β = 105.39 c = 43.136 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 CCD ADSC QUANTUM 210 mirrors 2002-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.4 39 93.8 0.063 26.3 6.6 44547 -3 13.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.4 1.45 90.6 0.255 10.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 MOLECULAR REPLACEMENT THROUGHOUT PBD ENTRY 1QI7 1.4 36.22 44520 44520 2235 93.5 0.1841 0.1841 0.184 0.1877 0.206 0.2104 RANDOM 15.2
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] -1.42 -1.8 3.26 -1.84
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.7 c_scangle_it 2.4 c_scbond_it 1.71 c_mcangle_it 1.57 c_angle_deg 1.2 c_mcbond_it 1.01 c_improper_angle_d 0.79 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.7 c_scangle_it 2.4 c_scbond_it 1.71 c_mcangle_it 1.57 c_angle_deg 1.2 c_mcbond_it 1.01 c_improper_angle_d 0.79 c_bond_d 0.008 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 2063 Nucleic Acid Atoms Solvent Atoms 487 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing CNS refinement