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Crystal structure of human Histidine Triad Nucleotide-Binding Protein 1 in complex with N-(2-hydroxyethyl)morpholino adenosine 6'-O-phosphate
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 MES pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.09 41.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.47 α = 90 b = 46.461 β = 94.523 c = 64.266 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 2026-07-20 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) 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 1.72 18.515 99.4 0.138 0.084 0.978 5.7 3.3 24235 7.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.72 1.75 99.6 0.286 0.228 0.841 2.1 2.2
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 1.72 18.515 24203 1115 99.201 0.189 0.1862 0.198 0.2418 0.251 9.591
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] 1.37 -0.383 -1.242 -0.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.222 r_dihedral_angle_3_deg 13.082 r_dihedral_angle_1_deg 6.287 r_dihedral_angle_2_deg 5.503 r_lrange_it 4.391 r_lrange_other 3.849 r_scangle_it 1.879 r_scangle_other 1.879 r_angle_refined_deg 1.643 r_mcangle_it 1.288
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.222 r_dihedral_angle_3_deg 13.082 r_dihedral_angle_1_deg 6.287 r_dihedral_angle_2_deg 5.503 r_lrange_it 4.391 r_lrange_other 3.849 r_scangle_it 1.879 r_scangle_other 1.879 r_angle_refined_deg 1.643 r_mcangle_it 1.288 r_mcangle_other 1.288 r_scbond_it 1.171 r_scbond_other 1.17 r_mcbond_it 0.776 r_mcbond_other 0.776 r_angle_other_deg 0.593 r_nbd_refined 0.261 r_symmetry_nbd_other 0.193 r_xyhbond_nbd_refined 0.188 r_symmetry_xyhbond_nbd_refined 0.188 r_nbd_other 0.173 r_nbtor_refined 0.168 r_symmetry_nbd_refined 0.139 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.048 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 348 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing