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Crystal structure of human Histidine Triad Nucleotide-Binding Protein 1 in complex with 5'-O-[N-(3-Indolepropionic acid)sulfamoyl] N2-methyl-2-aminoethenoadenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YQM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 281 10% w/v PEG4000, 0.1 M sodium cacodylate pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.07 40.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.675 α = 90 b = 46.434 β = 94.624 c = 63.788 γ = 90
Symmetry Space Group C 1 2 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 RIGAKU HyPix-6000HE 2023-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU PhotonJet-S 1.54184
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 1.8 19.041 99.8 0.087 0.096 0.039 0.997 12.6 5.7 21127 10
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 1.8 1.84 99.8 0.369 0.435 0.226 0.893 3.5
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 THROUGHOUT 1.8 19.041 21112 982 99.688 0.151 0.1494 0.1637 0.1906 0.1992 13.439
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] 1.55 -0.247 -0.729 -0.771
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.498 r_dihedral_angle_3_deg 14.207 r_dihedral_angle_1_deg 6.63 r_lrange_it 5.811 r_dihedral_angle_2_deg 5.732 r_lrange_other 5.598 r_scangle_it 3.332 r_scangle_other 3.33 r_scbond_it 2.205 r_scbond_other 2.205
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.498 r_dihedral_angle_3_deg 14.207 r_dihedral_angle_1_deg 6.63 r_lrange_it 5.811 r_dihedral_angle_2_deg 5.732 r_lrange_other 5.598 r_scangle_it 3.332 r_scangle_other 3.33 r_scbond_it 2.205 r_scbond_other 2.205 r_mcangle_it 1.973 r_mcangle_other 1.972 r_angle_refined_deg 1.528 r_mcbond_it 1.259 r_mcbond_other 1.256 r_angle_other_deg 0.531 r_nbd_refined 0.224 r_symmetry_nbd_refined 0.205 r_symmetry_xyhbond_nbd_refined 0.201 r_symmetry_nbd_other 0.196 r_xyhbond_nbd_refined 0.174 r_nbtor_refined 0.173 r_nbd_other 0.146 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1767 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing