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Apo Crystal Structure of a Substrate Binding Protein (IseP) from an Isethionate TRAP Transporter
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 293.15 Sodium bromide, Bis-Tris propane, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2 38.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.925 α = 90 b = 72.997 β = 90 c = 95.24 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 EIGER X 16M 2022-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95372 Australian Synchrotron MX2
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 1.48 47.665 100 0.066 0.07 0.021 0.999 25.6 19.8 50754
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 1.48 1.51 0.539 0.566 0.174 0.975 20.5
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 NONE 1.48 47.665 50684 2541 99.984 0.172 0.17 0.17 0.203 0.2029 23
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] 1.288 -0.181 -1.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.249 r_dihedral_angle_3_deg 12.445 r_dihedral_angle_2_deg 8.687 r_lrange_it 5.651 r_dihedral_angle_1_deg 5.63 r_lrange_other 5.582 r_scangle_it 4.608 r_scangle_other 4.607 r_scbond_it 3.164 r_scbond_other 3.164
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.249 r_dihedral_angle_3_deg 12.445 r_dihedral_angle_2_deg 8.687 r_lrange_it 5.651 r_dihedral_angle_1_deg 5.63 r_lrange_other 5.582 r_scangle_it 4.608 r_scangle_other 4.607 r_scbond_it 3.164 r_scbond_other 3.164 r_mcangle_other 2.329 r_mcangle_it 2.317 r_angle_refined_deg 2.018 r_mcbond_it 1.705 r_mcbond_other 1.701 r_angle_other_deg 0.683 r_nbd_refined 0.255 r_symmetry_nbd_refined 0.247 r_nbd_other 0.236 r_xyhbond_nbd_refined 0.214 r_symmetry_nbd_other 0.198 r_symmetry_xyhbond_nbd_other 0.192 r_symmetry_xyhbond_nbd_refined 0.186 r_nbtor_refined 0.184 r_chiral_restr 0.105 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2404 Nucleic Acid Atoms Solvent Atoms 393 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement MOLREP phasing