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The E74Q mutant of Small Alarmone Hydrolase SAH from Pseudomonas aeruginosa PAO1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Z3N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 14.6 mg/mL of PaSpo2 E74Q variant protein stock in the buffer of 25 mM Tris pH 8.0, 200 mM NaCl, 10 mM ppGpp and 10 mM MnCl2 is mixed 1:1 ratio with the precipitant consisted of 4.0 M NH4OAc, 0.1 M Bis-Tris propane, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.41 48.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.15 α = 90 b = 86.05 β = 101.77 c = 122.58 γ = 90
Symmetry Space Group C 1 2 1
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 EIGER2 XE 16M 2019-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.74 57.28 89.6 0.994 7.3 3.8 89102
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.74 1.77 99.9 0.422 1
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6Z3N 1.74 43.062 89102 4527 99.254 0.156 0.1518 0.1608 0.2274 0.2325 29.11
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] 1.702 -0.033 2.318 -3.686
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.733 r_dihedral_angle_4_deg 18.113 r_dihedral_angle_3_deg 13.121 r_scangle_it 7.1 r_scangle_other 7.099 r_lrange_it 6.953 r_lrange_other 6.872 r_scbond_it 6.388 r_scbond_other 6.385 r_dihedral_angle_1_deg 6.038
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.733 r_dihedral_angle_4_deg 18.113 r_dihedral_angle_3_deg 13.121 r_scangle_it 7.1 r_scangle_other 7.099 r_lrange_it 6.953 r_lrange_other 6.872 r_scbond_it 6.388 r_scbond_other 6.385 r_dihedral_angle_1_deg 6.038 r_mcangle_it 5.318 r_mcangle_other 5.317 r_rigid_bond_restr 4.984 r_mcbond_it 4.532 r_mcbond_other 4.532 r_angle_refined_deg 1.766 r_angle_other_deg 1.507 r_nbd_refined 0.223 r_symmetry_xyhbond_nbd_refined 0.202 r_nbd_other 0.191 r_symmetry_nbd_other 0.182 r_xyhbond_nbd_refined 0.175 r_nbtor_refined 0.164 r_symmetry_nbd_refined 0.146 r_symmetry_xyhbond_nbd_other 0.113 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5638 Nucleic Acid Atoms Solvent Atoms 526 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing