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Crystal structure of lychnin a type 1 Ribosome Inactivating Protein (RIP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WUC PDB ENTRY 1WUC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 30% PEG 8000, 0.1M sodium phosphate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.97 37.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.247 α = 90 b = 57.333 β = 106.25 c = 53.23 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 MARRESEARCH mirrors 2002-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.0 ELETTRA 5.2R
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 1.7 29.1 51 0.048 39.7 6.9 22021 21895 3 -3 13.8
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) 1.7 1.76 50.2 0.084 14.2 2162
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 PDB ENTRY 1WUC 1.7 28.44 22502 21878 2170 97.2 0.164 0.162 0.162 0.1634 0.196 0.2 RANDOM 13.6
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] 1.65 -1.14 -0.5 -1.15
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.4 c_scangle_it 2.68 c_scbond_it 1.9 c_mcangle_it 1.35 c_angle_deg 1.2 c_mcbond_it 0.98 c_improper_angle_d 0.64 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1863 Nucleic Acid Atoms Solvent Atoms 364 Heterogen Atoms
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing