☰ Navigation Tabs
S1 nuclease from Aspergillus oryzae in complex with two molecules of 2'-deoxycytidine-5'-monophosphate
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 3.8 291 0.1 M Citric acid pH 3.8, 25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 1.81 32.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.742 α = 90 b = 62.388 β = 90 c = 62.762 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 PIXEL DECTRIS PILATUS 6M 2014-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91842 BESSY 14.1
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 1.04 44.25 94.5 0.089 10.7 6 96234 4.8
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 1.04 1.06 54.5 0.307 2.7 2.3
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 1.04 44.25 96142 4712 94.46 0.11315 0.11106 0.1123 0.13509 0.127 Random selection 8.324
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] -0.54 0.32 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.967 r_sphericity_free 21.937 r_dihedral_angle_4_deg 11.661 r_dihedral_angle_3_deg 11.187 r_rigid_bond_restr 8.247 r_dihedral_angle_1_deg 5.948 r_sphericity_bonded 5.778 r_long_range_B_refined 2.764 r_angle_other_deg 2.067 r_long_range_B_other 1.992
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.967 r_sphericity_free 21.937 r_dihedral_angle_4_deg 11.661 r_dihedral_angle_3_deg 11.187 r_rigid_bond_restr 8.247 r_dihedral_angle_1_deg 5.948 r_sphericity_bonded 5.778 r_long_range_B_refined 2.764 r_angle_other_deg 2.067 r_long_range_B_other 1.992 r_angle_refined_deg 1.695 r_scangle_other 1.238 r_scbond_other 0.933 r_scbond_it 0.932 r_mcangle_it 0.831 r_mcangle_other 0.83 r_mcbond_it 0.612 r_mcbond_other 0.602 r_chiral_restr 0.107 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.009 r_bond_other_d 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2049 Nucleic Acid Atoms Solvent Atoms 485 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing Coot model building