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Crystal Structure of Substrate Binding Protein of Thermus thermophilus TAXI-TRAP protein with L-glutamate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1US4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293.15 Ammonium citrate dibasic, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.12 42.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.547 α = 90 b = 67.913 β = 90 c = 81.17 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 2023-08-05 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 1.11 43.552 99.7 0.08 0.087 0.033 0.999 14.1 12.8 112678
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 1.11 1.13 1.449 0.061 0.65 0.637 11.2
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.11 43.51 112590 5583 99.705 0.121 0.1201 0.1378 0.1372 14.478
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] -0.505 0.195 0.31
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 34.018 r_lrange_other 30.771 r_dihedral_angle_6_deg 15.832 r_dihedral_angle_3_deg 12.464 r_dihedral_angle_2_deg 11.063 r_scangle_it 9.36 r_scangle_other 9.358 r_dihedral_angle_1_deg 6.734 r_scbond_it 6.492 r_scbond_other 6.49
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 34.018 r_lrange_other 30.771 r_dihedral_angle_6_deg 15.832 r_dihedral_angle_3_deg 12.464 r_dihedral_angle_2_deg 11.063 r_scangle_it 9.36 r_scangle_other 9.358 r_dihedral_angle_1_deg 6.734 r_scbond_it 6.492 r_scbond_other 6.49 r_mcangle_it 6.331 r_mcangle_other 6.329 r_mcbond_it 4.336 r_mcbond_other 4.334 r_rigid_bond_restr 4.146 r_angle_refined_deg 2.03 r_angle_other_deg 0.672 r_symmetry_xyhbond_nbd_refined 0.548 r_xyhbond_nbd_other 0.402 r_symmetry_nbd_refined 0.367 r_nbd_refined 0.281 r_xyhbond_nbd_refined 0.23 r_nbd_other 0.217 r_symmetry_nbd_other 0.206 r_nbtor_refined 0.185 r_symmetry_xyhbond_nbd_other 0.169 r_chiral_restr 0.098 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2241 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement MOLREP phasing Coot model building XDS data reduction Aimless data scaling