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S1 nuclease from Aspergillus oryzae with unoccupied active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other our previous model of S1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 0.2 M Sodium chloride, 0.05 M Calcium chloride, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.17 43.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.184 α = 107.37 b = 48.595 β = 90.13 c = 65.469 γ = 105.72
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2015-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.0 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.5 43.05 88.2 0.06 9.2 1.8 68828 5.8
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 1.5 1.53 54.6 0.187 3.8 1.8
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 our previous model of S1 1.5 43.05 68827 3364 88.22 0.14963 0.14877 0.1486 0.17736 0.1649 Random selection 13.322
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] -1.07 0.18 0.11 0.97 0.01 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.948 r_dihedral_angle_3_deg 11.398 r_dihedral_angle_4_deg 8.639 r_dihedral_angle_1_deg 5.715 r_long_range_B_refined 4.825 r_long_range_B_other 4.135 r_scangle_other 2.179 r_angle_refined_deg 1.647 r_scbond_it 1.48 r_scbond_other 1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.948 r_dihedral_angle_3_deg 11.398 r_dihedral_angle_4_deg 8.639 r_dihedral_angle_1_deg 5.715 r_long_range_B_refined 4.825 r_long_range_B_other 4.135 r_scangle_other 2.179 r_angle_refined_deg 1.647 r_scbond_it 1.48 r_scbond_other 1.48 r_angle_other_deg 1.376 r_mcangle_it 1.354 r_mcangle_other 1.354 r_mcbond_it 0.904 r_mcbond_other 0.899 r_chiral_restr 0.109 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.007 r_gen_planes_other 0.004 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4084 Nucleic Acid Atoms Solvent Atoms 871 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing Coot model building