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Crystal structure of human Histidine Triad Nucleotide-Binding Protein 1 in complex with 5'-O-[(3-Indolyl)-1-Ethyl]Carbamoyl 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 12% w/v PEG4000, 0.1 M sodium cacodylate pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.1 41.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.597 α = 90 b = 46.314 β = 94.707 c = 64.01 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 2023-02-09 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 1.5 18.451 99.8 0.062 0.068 0.028 0.999 14.2 5.1 36820 9
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 1.5 1.53 98.9 0.503 0.598 0.315 0.84 2.3 2.3
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 1.5 18.451 36815 1878 99.702 0.151 0.149 0.1514 0.1794 0.1815 11.513
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] 1.353 -0.171 -0.48 -0.834
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.715 r_dihedral_angle_3_deg 14.721 r_dihedral_angle_2_deg 12.742 r_dihedral_angle_1_deg 6.14 r_lrange_it 5.051 r_lrange_other 4.721 r_scangle_it 2.881 r_scangle_other 2.88 r_mcangle_it 1.934 r_mcangle_other 1.933
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.715 r_dihedral_angle_3_deg 14.721 r_dihedral_angle_2_deg 12.742 r_dihedral_angle_1_deg 6.14 r_lrange_it 5.051 r_lrange_other 4.721 r_scangle_it 2.881 r_scangle_other 2.88 r_mcangle_it 1.934 r_mcangle_other 1.933 r_scbond_it 1.877 r_scbond_other 1.877 r_angle_refined_deg 1.657 r_mcbond_it 1.213 r_mcbond_other 1.21 r_angle_other_deg 0.606 r_symmetry_nbd_refined 0.264 r_nbd_refined 0.232 r_symmetry_nbd_other 0.201 r_symmetry_xyhbond_nbd_refined 0.2 r_xyhbond_nbd_refined 0.195 r_nbtor_refined 0.177 r_nbd_other 0.156 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1762 Nucleic Acid Atoms Solvent Atoms 332 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing