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Crystal structure of human Histidine Triad Nucleotide-Binding Protein 1 in complex with 5'-O-[(3-Indolyl)-1-Ethyl]Carbamoyl 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 2.11 41.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.845 α = 90 b = 46.324 β = 94.799 c = 63.971 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 2022-09-23 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 1.58 19.101 99.9 0.074 0.082 0.035 0.998 15.3 5.4 31671 8.2
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 1.58 1.61 100 0.661 0.775 0.396 0.742 2.1 3.6
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 1.58 19.101 31671 1625 99.912 0.15 0.1474 0.1621 0.1913 0.1993 10.824
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] 1.397 -0.114 -0.473 -0.893
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.953 r_dihedral_angle_3_deg 14.214 r_dihedral_angle_2_deg 7.088 r_dihedral_angle_1_deg 6.217 r_lrange_it 5.488 r_lrange_other 4.783 r_scangle_it 2.558 r_scangle_other 2.558 r_mcangle_it 1.705 r_mcangle_other 1.704
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.953 r_dihedral_angle_3_deg 14.214 r_dihedral_angle_2_deg 7.088 r_dihedral_angle_1_deg 6.217 r_lrange_it 5.488 r_lrange_other 4.783 r_scangle_it 2.558 r_scangle_other 2.558 r_mcangle_it 1.705 r_mcangle_other 1.704 r_scbond_it 1.656 r_scbond_other 1.656 r_angle_refined_deg 1.54 r_mcbond_it 1.091 r_mcbond_other 1.09 r_angle_other_deg 0.547 r_nbd_refined 0.244 r_symmetry_nbd_other 0.202 r_xyhbond_nbd_refined 0.188 r_symmetry_xyhbond_nbd_refined 0.183 r_nbtor_refined 0.175 r_symmetry_nbd_refined 0.162 r_dihedral_angle_other_2_deg 0.143 r_nbd_other 0.138 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1766 Nucleic Acid Atoms Solvent Atoms 390 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing