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S1 nuclease from Aspergillus oryzae in complex with cytidine-5'-monophosphate
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 2.09 41.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.075 α = 107.47 b = 48.459 β = 90.076 c = 65.547 γ = 105.702
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 1.04 44.358 84.5 0.053 0.999 10.8 3.6 196791 -3.7 6.6
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 1.04 1.06 42.2 0.505 0.829
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 1.04 44.358 196789 9747 84.456 0.11 0.1097 0.1087 0.1095 0.1307 0.1117 Random 11.107
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] 0.041 -0.043 0.01 0.024 -0.048 -0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.446 r_dihedral_angle_3_deg 10.802 r_dihedral_angle_4_deg 8.625 r_dihedral_angle_1_deg 6.279 r_rigid_bond_restr 2.574 r_angle_refined_deg 1.775 r_angle_other_deg 1.717 r_scangle_it 1.687 r_scangle_other 1.687 r_scbond_it 1.514
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.446 r_dihedral_angle_3_deg 10.802 r_dihedral_angle_4_deg 8.625 r_dihedral_angle_1_deg 6.279 r_rigid_bond_restr 2.574 r_angle_refined_deg 1.775 r_angle_other_deg 1.717 r_scangle_it 1.687 r_scangle_other 1.687 r_scbond_it 1.514 r_mcangle_other 1.039 r_mcangle_it 1.03 r_mcbond_other 0.843 r_mcbond_it 0.832 r_symmetry_nbd_refined 0.238 r_nbd_refined 0.229 r_nbd_other 0.202 r_nbtor_refined 0.186 r_symmetry_nbd_other 0.172 r_symmetry_xyhbond_nbd_refined 0.162 r_xyhbond_nbd_refined 0.146 r_metal_ion_refined 0.131 r_chiral_restr 0.105 r_symmetry_nbtor_other 0.091 r_symmetry_xyhbond_nbd_other 0.075 r_chiral_restr_other 0.035 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4075 Nucleic Acid Atoms Solvent Atoms 898 Heterogen Atoms 175
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing Coot model building