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Crystal Structure of the Substrate Binding Domain Protein of the ABC Transporter PBP2_YxeM from Vibrio cholerae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 1.6 M Lithium sulfate, 150 mM Cacodylate pH 6.5, 1.0 % v/v 1,2 propanediol
Crystal Properties Matthews coefficient Solvent content 2.83 56.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.044 α = 90 b = 105.816 β = 119.922 c = 118.124 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 100 PIXEL DECTRIS PILATUS3 X 6M 2017-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97934 APS 19-ID
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 2.3 59.11 95.8 0.114 0.141 0.082 0.8764 7.4 2.9 107373
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 2.3 2.34 0.469 0.578 0.333 0.565 2.1
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 MOLECULAR REPLACEMENT FREE R-VALUE 2.3 59.11 107297 5579 95.487 0.196 0.1938 0.1927 0.2285 0.2266 27.931
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] -18.861 1.701 35.709 -16.849
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.337 r_dihedral_angle_3_deg 14.133 r_dihedral_angle_1_deg 4.161 r_lrange_it 3.215 r_lrange_other 3.2 r_mcangle_it 2.75 r_mcangle_other 2.749 r_scangle_it 1.847 r_scangle_other 1.846 r_mcbond_it 1.767
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.337 r_dihedral_angle_3_deg 14.133 r_dihedral_angle_1_deg 4.161 r_lrange_it 3.215 r_lrange_other 3.2 r_mcangle_it 2.75 r_mcangle_other 2.749 r_scangle_it 1.847 r_scangle_other 1.846 r_mcbond_it 1.767 r_mcbond_other 1.767 r_angle_refined_deg 1.261 r_scbond_it 1.234 r_scbond_other 1.233 r_dihedral_angle_2_deg 0.787 r_angle_other_deg 0.579 r_symmetry_xyhbond_nbd_refined 0.24 r_metal_ion_refined 0.231 r_symmetry_nbd_other 0.219 r_nbd_other 0.203 r_xyhbond_nbd_refined 0.187 r_nbd_refined 0.181 r_nbtor_refined 0.177 r_symmetry_nbd_refined 0.114 r_symmetry_xyhbond_nbd_other 0.091 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.053 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15930 Nucleic Acid Atoms Solvent Atoms 648 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling HKL-3000 phasing MOLREP phasing