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Crystal structure of human Histidine Triad Nucleotide-Binding Protein 1 in complex with 5'-O-[(3-Indolyl)-1-Ethyl]Carbamoyl Ethenoadenosine
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 2.12 41.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.725 α = 90 b = 46.552 β = 94.738 c = 64.101 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 2023-02-07 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 1.9 19.22 99.6 0.1 0.116 0.057 0.994 8.9 3.9 18317 10.9
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 1.9 1.94 98.7 0.331 0.4 0.22 0.891 2.5 2.9
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 1.9 19.22 18298 910 99.381 0.156 0.1544 0.1676 0.19 0.1993 14.134
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] 1.89 -0.4 -0.491 -1.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.604 r_dihedral_angle_3_deg 14.792 r_dihedral_angle_1_deg 6.422 r_dihedral_angle_2_deg 5.238 r_lrange_it 4.735 r_lrange_other 4.487 r_scangle_it 3.08 r_scangle_other 3.079 r_mcangle_it 1.964 r_mcangle_other 1.964
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.604 r_dihedral_angle_3_deg 14.792 r_dihedral_angle_1_deg 6.422 r_dihedral_angle_2_deg 5.238 r_lrange_it 4.735 r_lrange_other 4.487 r_scangle_it 3.08 r_scangle_other 3.079 r_mcangle_it 1.964 r_mcangle_other 1.964 r_scbond_it 1.883 r_scbond_other 1.882 r_angle_refined_deg 1.461 r_mcbond_it 1.272 r_mcbond_other 1.27 r_angle_other_deg 0.505 r_nbd_refined 0.241 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.17 r_symmetry_xyhbond_nbd_refined 0.159 r_nbd_other 0.136 r_symmetry_nbd_refined 0.094 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1762 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing