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S1 nuclease from Aspergillus oryzae in complex with uridine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FB9
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, protein concentration 10 mg/ml
Crystal Properties Matthews coefficient Solvent content 1.99 38.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.04 α = 107.184 b = 48.186 β = 90.114 c = 65.232 γ = 105.618
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 2016-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.0332 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 1.06 44.2 86.02 0.085 0.997 8 3.6 187610 -3.7 9.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.06 1.088 64.47 1.145 0.373 1.2 3.4
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 (All) 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 5FB9 1.06 44.2 187610 9423 86.015 0.12 0.1205 0.1181 0.1202 0.1468 0.1252 Random 13.44
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] -0.498 -0.01 -0.011 0.272 0.095 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.339 r_dihedral_angle_3_deg 11.128 r_dihedral_angle_4_deg 9.861 r_dihedral_angle_1_deg 6.17 r_dihedral_angle_other_3_deg 4.494 r_rigid_bond_restr 2.495 r_scangle_it 1.914 r_scangle_other 1.914 r_angle_other_deg 1.716 r_scbond_it 1.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.339 r_dihedral_angle_3_deg 11.128 r_dihedral_angle_4_deg 9.861 r_dihedral_angle_1_deg 6.17 r_dihedral_angle_other_3_deg 4.494 r_rigid_bond_restr 2.495 r_scangle_it 1.914 r_scangle_other 1.914 r_angle_other_deg 1.716 r_scbond_it 1.67 r_angle_refined_deg 1.658 r_mcangle_other 1.308 r_mcangle_it 1.295 r_mcbond_it 1.047 r_mcbond_other 1.031 r_symmetry_nbd_refined 0.243 r_nbd_refined 0.233 r_nbd_other 0.207 r_nbtor_refined 0.183 r_symmetry_nbd_other 0.172 r_symmetry_xyhbond_nbd_refined 0.142 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.104 r_metal_ion_refined 0.091 r_symmetry_nbtor_other 0.088 r_bond_refined_d 0.011 r_bond_other_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4075 Nucleic Acid Atoms Solvent Atoms 770 Heterogen Atoms 135
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing Coot model building