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Crystal structure of the sulfoquinovosyl binding protein SmoF complexed with sulfoquinovosyl diacylglycerol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7QHU D_1292119394
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 279 0.2M L-Na-glutamate, alanine, glycine, lysine hydrochloride, serine, 0.1M TRIS, bicine, 12.5% MPD, PEG1000, PEG3350
Crystal Properties Matthews coefficient Solvent content 2.2 43.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.215 α = 90 b = 69.589 β = 91.539 c = 104.574 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 210 PIXEL DECTRIS PILATUS 6M-F 2019-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97933 Diamond I04
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 2.14 69.59 99.9 0.093 0.124 0.081 0.992 8.9 4.1 42301
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 2.14 2.2 0.305 0.406 0.265 0.942 4.1
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 D_1292119394 2.14 57.995 42277 2124 99.865 0.206 0.2035 0.2056 0.2598 0.2627 24.287
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] 3.124 3.128 -0.769 -2.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.392 r_dihedral_angle_4_deg 22.688 r_dihedral_angle_3_deg 14.801 r_dihedral_angle_1_deg 6.61 r_lrange_it 4.222 r_lrange_other 4.204 r_scangle_it 2.884 r_scangle_other 2.883 r_mcangle_it 2.553 r_mcangle_other 2.553
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.392 r_dihedral_angle_4_deg 22.688 r_dihedral_angle_3_deg 14.801 r_dihedral_angle_1_deg 6.61 r_lrange_it 4.222 r_lrange_other 4.204 r_scangle_it 2.884 r_scangle_other 2.883 r_mcangle_it 2.553 r_mcangle_other 2.553 r_scbond_it 1.887 r_scbond_other 1.885 r_mcbond_other 1.677 r_mcbond_it 1.676 r_angle_refined_deg 1.504 r_angle_other_deg 1.3 r_symmetry_xyhbond_nbd_refined 0.214 r_nbd_refined 0.201 r_symmetry_nbd_other 0.179 r_nbd_other 0.173 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.155 r_symmetry_nbd_refined 0.111 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.069 r_symmetry_xyhbond_nbd_other 0.043 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5828 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling MOLREP phasing