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S1 nuclease from Aspergillus oryzae in complex with phosphate and 2'-deoxycytidine
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, HANGING 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 1.95 36.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.04 α = 90 b = 62.426 β = 90 c = 84.118 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 120 CCD AGILENT ATLAS CCD 2013-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.54056
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 1.75 30.08 95.2 0.061 13.6 3.7 22221 5.1
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 1.75 1.78 72.2 0.376 2.1 2.2
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 1.75 30.08 22191 1138 94.27 0.15288 0.1515 0.1643 0.21159 0.1932 Random selection 11.744
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] 0.56 -0.84 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.507 r_dihedral_angle_3_deg 13.175 r_dihedral_angle_4_deg 12.895 r_dihedral_angle_1_deg 5.69 r_long_range_B_refined 4.753 r_long_range_B_other 4.298 r_scangle_other 1.99 r_angle_refined_deg 1.706 r_mcangle_other 1.363 r_mcangle_it 1.361
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.507 r_dihedral_angle_3_deg 13.175 r_dihedral_angle_4_deg 12.895 r_dihedral_angle_1_deg 5.69 r_long_range_B_refined 4.753 r_long_range_B_other 4.298 r_scangle_other 1.99 r_angle_refined_deg 1.706 r_mcangle_other 1.363 r_mcangle_it 1.361 r_scbond_it 1.318 r_scbond_other 1.317 r_angle_other_deg 1.1 r_mcbond_it 0.88 r_mcbond_other 0.873 r_chiral_restr 0.119 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2049 Nucleic Acid Atoms Solvent Atoms 377 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing Coot model building