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Crystal structure of a solute receptor from Synechococcus CC9311 in complex with alpha-ketovaleric and calcium
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 0.02 M Sodium/Potassium Phosphate, 0.1M Bis Tris propane 7.5, 20% Peg 3350
Cryo: 30 % Peg 400
Crystal Properties Matthews coefficient Solvent content 2.05 39.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.68 α = 69.649 b = 54.75 β = 77.732 c = 61.15 γ = 67.267
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 50 PIXEL DECTRIS PILATUS 12M 2019-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I23 2.7552, 3.1790, 3.4925, 4.7686 Diamond I23
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.796 50.277 90.9 0.068 0.073 0.024 0.999 16.8 13.6 50762
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 9.06 50.23 0.039 0.041 0.012 0.999 23.3
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 SAD FREE R-VALUE 1.796 50.277 50762 2454 89.014 0.17 0.1687 0.1689 0.1898 0.1904 44.394
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] 2.341 -1.224 -0.948 -1.642 1.715 -0.183
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.739 r_dihedral_angle_3_deg 15.109 r_dihedral_angle_4_deg 13.801 r_lrange_other 8.054 r_lrange_it 8.05 r_scangle_it 6.79 r_scangle_other 6.79 r_dihedral_angle_1_deg 6.345 r_mcangle_it 5.008 r_mcangle_other 5.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.739 r_dihedral_angle_3_deg 15.109 r_dihedral_angle_4_deg 13.801 r_lrange_other 8.054 r_lrange_it 8.05 r_scangle_it 6.79 r_scangle_other 6.79 r_dihedral_angle_1_deg 6.345 r_mcangle_it 5.008 r_mcangle_other 5.008 r_scbond_it 4.753 r_scbond_other 4.748 r_mcbond_it 3.873 r_mcbond_other 3.867 r_angle_refined_deg 1.509 r_angle_other_deg 1.375 r_symmetry_xyhbond_nbd_refined 0.263 r_nbd_other 0.205 r_nbd_refined 0.201 r_symmetry_nbd_other 0.181 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.152 r_symmetry_nbd_refined 0.129 r_symmetry_xyhbond_nbd_other 0.111 r_metal_ion_refined 0.108 r_ncsr_local_group_1 0.097 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5159 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling CRANK2 phasing Coot model building