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Crystal structure of the sulfoquinovosyl binding protein SmoF complexed with SQMe
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7OFY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.3 M sodium acetate,
0.1 M BIS-TRIS (pH 5.5) and 35% PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 2.01 38.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.27 α = 90 b = 99.38 β = 90 c = 53.76 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 6M-F 2019-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 1.59 47.33 99.4 0.28 0.302 0.148 0.98 7.7 6.9 48233
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 1.59 1.62 0.679 5.6
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 70FY 1.59 47.33 48179 2429 99.234 0.239 0.2377 0.2381 0.2669 0.2685 18.698
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] -0.85 2.683 -1.833
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.259 r_dihedral_angle_4_deg 20.047 r_dihedral_angle_3_deg 13.227 r_dihedral_angle_1_deg 6.422 r_lrange_it 3.919 r_lrange_other 3.796 r_scangle_it 2.611 r_scangle_other 2.611 r_mcangle_it 1.853 r_mcangle_other 1.853
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.259 r_dihedral_angle_4_deg 20.047 r_dihedral_angle_3_deg 13.227 r_dihedral_angle_1_deg 6.422 r_lrange_it 3.919 r_lrange_other 3.796 r_scangle_it 2.611 r_scangle_other 2.611 r_mcangle_it 1.853 r_mcangle_other 1.853 r_scbond_it 1.784 r_scbond_other 1.784 r_angle_refined_deg 1.507 r_angle_other_deg 1.383 r_mcbond_it 1.265 r_mcbond_other 1.264 r_nbd_refined 0.214 r_nbd_other 0.19 r_symmetry_xyhbond_nbd_refined 0.181 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.158 r_symmetry_nbd_refined 0.1 r_chiral_restr 0.076 r_symmetry_nbtor_other 0.076 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 2915 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction MOLREP phasing