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Y81W mutant of RNase Sa from Streptomyces aureofaciens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RGG PDB entry 1rgg
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 295 ammonium sulfate, disodium phosphate, monosodium phosphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.3 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.206 α = 90 b = 64.309 β = 90 c = 77.666 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 100 IMAGE PLATE MARRESEARCH 2003-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 0.812 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 33.3 99.6 0.047 34.5 6.5 103514 10
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 1.01 97.7 0.165 10.2 4.5 4121
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1rgg 1 33 98348 5166 99.56 0.14631 0.14524 0.1547 0.16593 0.1738 RANDOM 8.056
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] 0.13 -0.33 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.078 r_sphericity_free 5.766 r_sphericity_bonded 4.166 r_scangle_it 2.912 r_scbond_it 2.068 r_mcangle_it 1.804 r_angle_refined_deg 1.478 r_mcbond_it 1.179 r_rigid_bond_restr 0.932 r_angle_other_deg 0.874
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.078 r_sphericity_free 5.766 r_sphericity_bonded 4.166 r_scangle_it 2.912 r_scbond_it 2.068 r_mcangle_it 1.804 r_angle_refined_deg 1.478 r_mcbond_it 1.179 r_rigid_bond_restr 0.932 r_angle_other_deg 0.874 r_symmetry_vdw_other 0.307 r_nbd_other 0.263 r_nbd_refined 0.233 r_xyhbond_nbd_refined 0.17 r_symmetry_vdw_refined 0.147 r_symmetry_hbond_refined 0.145 r_chiral_restr 0.091 r_nbtor_other 0.083 r_gen_planes_other 0.011 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1686 Nucleic Acid Atoms Solvent Atoms 589 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing