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Crystal structure of ligand free open conformation of sulfoquinovosyl binding protein (SQBP) from Agrobacterium tumefaciens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB D_1292108223
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 279 0.3 M Ammonium Acetate
0.1 M Bis-TRIS pH 5.5
25% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.2275825 44.81749
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.321 α = 109.039 b = 78.212 β = 106.865 c = 83.456 γ = 104.766
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 EIGER X 16M 2018-12-15 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 1.35 72.014 93.3 0.995 11.1 2.1 234884
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 1.35 1.37 0.906
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE D_1292108223 1.35 72.014 234883 11842 93.253 0.184 0.1832 0.2095 0.2134 14.291
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] 5.979 -2.035 1.372 -2.484 -0.188 -3.494
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.847 r_dihedral_angle_4_deg 17.957 r_dihedral_angle_3_deg 12.352 r_dihedral_angle_1_deg 5.625 r_lrange_it 4.149 r_lrange_other 4.149 r_scangle_it 3.122 r_scangle_other 3.122 r_angle_other_deg 2.373 r_scbond_it 2.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.847 r_dihedral_angle_4_deg 17.957 r_dihedral_angle_3_deg 12.352 r_dihedral_angle_1_deg 5.625 r_lrange_it 4.149 r_lrange_other 4.149 r_scangle_it 3.122 r_scangle_other 3.122 r_angle_other_deg 2.373 r_scbond_it 2.156 r_scbond_other 2.156 r_mcangle_other 1.874 r_mcangle_it 1.873 r_angle_refined_deg 1.833 r_mcbond_it 1.32 r_mcbond_other 1.312 r_nbd_other 0.337 r_symmetry_nbd_refined 0.329 r_nbd_refined 0.225 r_symmetry_nbd_other 0.205 r_nbtor_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.132 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.099 r_symmetry_nbtor_other 0.071 r_bond_other_d 0.036 r_gen_planes_other 0.016 r_bond_refined_d 0.014 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8804 Nucleic Acid Atoms Solvent Atoms 1464 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement DIALS data reduction autoPROC data scaling MOLREP phasing