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Structure of a HEPES bound TRAP transporter substrate binding protein.
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 0.1 M HEPES pH 7.5, 20% PEG 4000, 10% 2-Propanol
Crystal Properties Matthews coefficient Solvent content 2.12 42.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.588 α = 90 b = 73.208 β = 90 c = 94.818 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 2022-02-22 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 1.89 47.454 100 0.058 0.06 0.016 1 35.7 26.2 26163
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 1.89 1.93 0.471 0.49 0.132 0.982 26
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 NONE 1.89 47.454 26109 1371 99.973 0.178 0.1747 0.2294 0.2393 34.663
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] 2.847 -1.93 -0.917
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.936 r_dihedral_angle_3_deg 14.103 r_dihedral_angle_2_deg 8.444 r_lrange_it 7.701 r_scangle_it 7.033 r_dihedral_angle_1_deg 5.954 r_scbond_it 4.82 r_mcangle_it 3.782 r_mcbond_it 3.029 r_angle_refined_deg 1.961
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.936 r_dihedral_angle_3_deg 14.103 r_dihedral_angle_2_deg 8.444 r_lrange_it 7.701 r_scangle_it 7.033 r_dihedral_angle_1_deg 5.954 r_scbond_it 4.82 r_mcangle_it 3.782 r_mcbond_it 3.029 r_angle_refined_deg 1.961 r_nbtor_refined 0.313 r_symmetry_xyhbond_nbd_refined 0.222 r_nbd_refined 0.214 r_symmetry_nbd_refined 0.202 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.125 r_bond_refined_d 0.009 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2381 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement MOLREP phasing iMOSFLM data reduction Aimless data scaling