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Enzymatic and Structural Characterisation of Amphinase, a Novel Cytotoxic Ribonuclease from Rana pipiens Oocytes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Amphinase-2 (native)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 289 protein: 12.5 mg/ml, PEG 4000 30%, Na Citrate 0.1 M, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.01 38.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.795 α = 116.56 b = 44.607 β = 83.19 c = 46.054 γ = 103.68
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 MAR CCD 165 mm mirrors 2006-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
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 1.91 41.2 89.8 0.037 18.8 2.1 15432 14385 2 1 15
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) 1.91 2.01 63.5 0.108 7.5 1.9 1477
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 Amphinase-2 (native) 1.93 41.2 15432 14385 727 93.24 0.148 0.148 0.146 0.145 0.191 0.1895 RANDOM 14.63
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] 0.18 -1.18 -1.02 -0.18 0.05 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.762 r_dihedral_angle_4_deg 14.339 r_dihedral_angle_3_deg 12.879 r_dihedral_angle_1_deg 7.046 r_scangle_it 2.776 r_scbond_it 1.708 r_angle_refined_deg 1.224 r_mcangle_it 0.932 r_mcbond_it 0.485 r_nbtor_refined 0.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.762 r_dihedral_angle_4_deg 14.339 r_dihedral_angle_3_deg 12.879 r_dihedral_angle_1_deg 7.046 r_scangle_it 2.776 r_scbond_it 1.708 r_angle_refined_deg 1.224 r_mcangle_it 0.932 r_mcbond_it 0.485 r_nbtor_refined 0.292 r_nbd_refined 0.192 r_symmetry_hbond_refined 0.186 r_symmetry_vdw_refined 0.158 r_metal_ion_refined 0.148 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.087 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1797 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 42
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection MOSFLM data reduction SCALA data scaling