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Crystal structure of a Spermidine binding protein isolated from Synechococcus CC9311
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 20% (w/v) PEG 8000, 100 mM HEPES/ Sodium hydroxide pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.53 51.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.08 α = 90 b = 65.98 β = 98.633 c = 64.37 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS 12M 2020-06-26 M SINGLE WAVELENGTH 2 1 x-ray 80 PIXEL DECTRIS PILATUS 12M 2020-06-26 M SINGLE WAVELENGTH 3 1 x-ray 80 PIXEL DECTRIS PILATUS 12M 2020-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I23 2.7552 Diamond I23 2 SYNCHROTRON DIAMOND BEAMLINE I23 4.2753 Diamond I23 3 SYNCHROTRON DIAMOND BEAMLINE I23 4.5082 Diamond I23
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 1.796 45.847 90.3 0.999 19.6 11.4 27220
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 1.8 1.83 0.611
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD FREE R-VALUE 1.8 45.847 27216 1322 90.455 0.185 0.1831 0.1835 0.2194 0.2198 37.303
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] -1.131 0.428 0.879 0.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.603 r_dihedral_angle_6_deg 15.13 r_dihedral_angle_3_deg 14.45 r_lrange_it 9.239 r_lrange_other 9.198 r_dihedral_angle_1_deg 6.804 r_scangle_it 6.44 r_scangle_other 6.439 r_scbond_it 4.639 r_scbond_other 4.637
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.603 r_dihedral_angle_6_deg 15.13 r_dihedral_angle_3_deg 14.45 r_lrange_it 9.239 r_lrange_other 9.198 r_dihedral_angle_1_deg 6.804 r_scangle_it 6.44 r_scangle_other 6.439 r_scbond_it 4.639 r_scbond_other 4.637 r_mcangle_it 4.204 r_mcangle_other 4.202 r_mcbond_it 3.075 r_mcbond_other 3.073 r_angle_refined_deg 2.343 r_angle_other_deg 0.892 r_symmetry_nbd_refined 0.37 r_symmetry_xyhbond_nbd_refined 0.263 r_nbd_refined 0.225 r_symmetry_xyhbond_nbd_other 0.206 r_nbd_other 0.196 r_xyhbond_nbd_refined 0.176 r_nbtor_refined 0.169 r_symmetry_nbd_other 0.167 r_chiral_restr 0.123 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.016 r_gen_planes_refined 0.014 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2262 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling CRANK2 phasing