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Crystal structure of RNase Sa3,cytotoxic microbial ribonuclease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RGG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 293 sodium acetate, calcium acetate, acetic acid, MPD, ammonium sulphate, pH 4.2, VAPOR DIFFUSION, HANGING DROP at 293K
Crystal Properties Matthews coefficient Solvent content 1.9 37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.05 α = 90 b = 34.05 β = 90 c = 147.22 γ = 90
Symmetry Space Group P 41 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 293 IMAGE PLATE MARRESEARCH 1996-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 0.900 EMBL/DESY, HAMBURG BW7A
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 20 100 0.036 47.6 6.9 10355 22.2
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) 1.7 1.71 100 0.119 14 5.8 257
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1RGG 1.7 20 10286 10286 498 100 0.186 0.186 0.185 0.1945 0.224 RANDOM 23.9
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] -0.205 -0.205 0.411
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 16.054 r_sphericity_bonded 6.571 p_scangle_it 5.728 r_scangle_it 5.728 r_dihedral_angle_1_deg 5.398 p_scbond_it 3.88 r_scbond_it 3.88 p_mcangle_it 3.129 r_mcangle_it 3.129 p_mcbond_it 2.067
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 16.054 r_sphericity_bonded 6.571 p_scangle_it 5.728 r_scangle_it 5.728 r_dihedral_angle_1_deg 5.398 p_scbond_it 3.88 r_scbond_it 3.88 p_mcangle_it 3.129 r_mcangle_it 3.129 p_mcbond_it 2.067 r_mcbond_it 2.067 r_rigid_bond_restr 1.916 p_angle_deg 1.783 p_angle_d 1.783 r_angle_refined_deg 1.783 r_angle_other_deg 0.904 p_hb_or_metal_coord 0.199 p_chiral_restr 0.119 r_chiral_restr 0.119 p_bond_d 0.02 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001 p_planar_d p_plane_restr
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 769 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 5
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement