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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 7.6 293 Tris, HCl, HEPES, lithium sulphate, pH 7.6,
VAPOR DIFFUSION, HANGING DROP at 293K
Crystal Properties Matthews coefficient Solvent content 3.8 68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.72 α = 90 b = 64.72 β = 90 c = 69.57 γ = 120
Symmetry Space Group P 31 2 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 IMAGE PLATE MARRESEARCH 2000-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X31 1.100 EMBL/DESY, HAMBURG X31
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 2 29.6 100 0.06 31.6 9.5 11799 11799 28.5
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) 2 2.02 99.5 0.306 5.8 7.9 390
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 2 29 11799 11760 559 100 0.155 0.155 0.154 0.168 0.212 RANDOM 25.813
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] 2.09 1.05 2.09 -3.14
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 14.373 p_scangle_it 5.842 r_scangle_it 5.842 r_dihedral_angle_1_deg 5.479 r_sphericity_bonded 4.616 p_scbond_it 3.836 r_scbond_it 3.836 p_mcangle_it 2.56 r_mcangle_it 2.56 r_rigid_bond_restr 1.954
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 14.373 p_scangle_it 5.842 r_scangle_it 5.842 r_dihedral_angle_1_deg 5.479 r_sphericity_bonded 4.616 p_scbond_it 3.836 r_scbond_it 3.836 p_mcangle_it 2.56 r_mcangle_it 2.56 r_rigid_bond_restr 1.954 p_angle_deg 1.831 p_angle_d 1.831 r_angle_refined_deg 1.831 p_mcbond_it 1.642 r_mcbond_it 1.642 r_angle_other_deg 0.824 p_hb_or_metal_coord 0.171 p_chiral_restr 0.105 r_chiral_restr 0.105 p_bond_d 0.021 r_bond_refined_d 0.021 p_plane_restr 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.001 p_planar_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 782 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 1
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement