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Crystal structure of human Histidine Triad Nucleotide-Binding Protein 1 in complex with 5'-O-[N-(3-Indolepropionic acid)sulfamoyl] 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 14% w/v PEG4000, 0.1 M sodium cacodylate pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.13 42.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.192 α = 90 b = 46.55 β = 94.844 c = 64.105 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 2022-09-26 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 2.1 18.486 99.8 0.082 0.091 0.039 0.998 14.9 5.3 13742 10.3
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 2.1 2.16 99.9 0.229 0.254 0.108 0.963 5.4
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 2.1 18.486 13733 592 99.717 0.138 0.1357 0.1503 0.1874 0.1988 13.863
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] 1.983 -0.198 -0.522 -1.407
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.096 r_dihedral_angle_3_deg 14.259 r_dihedral_angle_2_deg 7.371 r_dihedral_angle_1_deg 6.852 r_lrange_it 5.041 r_lrange_other 4.787 r_scangle_it 2.902 r_scangle_other 2.901 r_mcangle_it 1.866 r_mcangle_other 1.866
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.096 r_dihedral_angle_3_deg 14.259 r_dihedral_angle_2_deg 7.371 r_dihedral_angle_1_deg 6.852 r_lrange_it 5.041 r_lrange_other 4.787 r_scangle_it 2.902 r_scangle_other 2.901 r_mcangle_it 1.866 r_mcangle_other 1.866 r_scbond_it 1.788 r_scbond_other 1.787 r_angle_refined_deg 1.461 r_mcbond_it 1.228 r_mcbond_other 1.227 r_angle_other_deg 0.495 r_symmetry_xyhbond_nbd_refined 0.237 r_nbd_refined 0.235 r_symmetry_nbd_other 0.194 r_xyhbond_nbd_refined 0.174 r_nbtor_refined 0.171 r_nbd_other 0.147 r_symmetry_nbd_refined 0.146 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.081 r_symmetry_xyhbond_nbd_other 0.049 r_dihedral_angle_other_2_deg 0.021 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1762 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing