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Structural and Thermodynamic Analyses of E. coli ribonuclease HI Variant with Quintuple Thermostabilizing Mutations
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RN2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 1.86 33.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.371 α = 90 b = 86.483 β = 90 c = 34.816 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 2006-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.80 SPring-8 BL38B1
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 1.32 50 99.8 0.032 62 31520
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 1.32 1.37 99.9 0.134 12.1
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 2RN2 1.4 25.91 26471 100 0.18243 0.18243 0.1861 11.709
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.114 r_dihedral_angle_1_deg 6.138 r_scangle_it 4.26 r_scbond_it 2.615 r_angle_refined_deg 1.876 r_mcangle_it 1.669 r_angle_other_deg 1.079 r_mcbond_it 0.947 r_chiral_restr 0.492 r_symmetry_vdw_refined 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.114 r_dihedral_angle_1_deg 6.138 r_scangle_it 4.26 r_scbond_it 2.615 r_angle_refined_deg 1.876 r_mcangle_it 1.669 r_angle_other_deg 1.079 r_mcbond_it 0.947 r_chiral_restr 0.492 r_symmetry_vdw_refined 0.44 r_symmetry_hbond_refined 0.435 r_xyhbond_nbd_refined 0.282 r_symmetry_vdw_other 0.26 r_nbd_refined 0.254 r_nbd_other 0.208 r_xyhbond_nbd_other 0.063 r_bond_refined_d 0.025 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1234 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing