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Crystal Structure of Substrate Binding Protein (TAXI-TRAP) in Complex with L-Glutamate from Bordetella pertussis
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 9.5 293.15 0.1 M CHES, 20% w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 1.91 41.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.43 α = 90 b = 76.913 β = 93.677 c = 65.233 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 EIGER X 16M 2025-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953732 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 2.008 45.998 99.3 0.085 0.101 0.054 0.997 12.3 6.8 37733
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 2.01 2.06 0.546 0.646 0.342 0.954 6.5
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 FREE R-VALUE 2.01 45.996 37713 1805 99.357 0.17 0.1648 0.1643 0.2781 0.2769 38.748
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] -3.719 -4.031 -1.15 5.343
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.918 r_dihedral_angle_3_deg 16.244 r_dihedral_angle_4_deg 16.112 r_lrange_it 9.735 r_lrange_other 9.732 r_rigid_bond_restr 9.529 r_scangle_other 7.984 r_scangle_it 7.983 r_mcangle_it 7.701 r_mcangle_other 7.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.918 r_dihedral_angle_3_deg 16.244 r_dihedral_angle_4_deg 16.112 r_lrange_it 9.735 r_lrange_other 9.732 r_rigid_bond_restr 9.529 r_scangle_other 7.984 r_scangle_it 7.983 r_mcangle_it 7.701 r_mcangle_other 7.7 r_dihedral_angle_1_deg 6.772 r_scbond_it 6.573 r_scbond_other 6.568 r_mcbond_it 5.932 r_mcbond_other 5.928 r_angle_refined_deg 1.502 r_angle_other_deg 1.305 r_nbd_other 0.233 r_symmetry_xyhbond_nbd_refined 0.22 r_symmetry_xyhbond_nbd_other 0.211 r_nbd_refined 0.2 r_symmetry_nbd_other 0.194 r_symmetry_nbd_refined 0.169 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.151 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.069 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4534 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement REFMAC refinement MOLREP phasing Coot model building Aimless data scaling XDS data reduction