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Crystal structure of human Histidine Triad Nucleotide-Binding Protein 1 in complex with KV30
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 2.09 41.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.011 α = 90 b = 46.467 β = 94.596 c = 63.839 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 2023-12-18 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 18.03 98.2 0.065 0.08 0.045 0.996 12.3 2.7 15270 12.6
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 2.05 99.5 0.206 0.251 0.141 0.944 4.8 2.8
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 2.001 18.03 15252 740 97.958 0.144 0.1413 0.1563 0.1875 0.1944 16.232
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] 2.312 -0.222 -0.332 -1.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.155 r_dihedral_angle_3_deg 13.319 r_dihedral_angle_2_deg 7.074 r_dihedral_angle_1_deg 6.506 r_lrange_it 5.817 r_lrange_other 5.593 r_scangle_it 3.789 r_scangle_other 3.701 r_scbond_it 2.42 r_scbond_other 2.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.155 r_dihedral_angle_3_deg 13.319 r_dihedral_angle_2_deg 7.074 r_dihedral_angle_1_deg 6.506 r_lrange_it 5.817 r_lrange_other 5.593 r_scangle_it 3.789 r_scangle_other 3.701 r_scbond_it 2.42 r_scbond_other 2.303 r_mcangle_it 2.033 r_mcangle_other 2.032 r_angle_refined_deg 1.631 r_mcbond_it 1.352 r_mcbond_other 1.352 r_angle_other_deg 0.56 r_nbd_refined 0.194 r_symmetry_nbd_other 0.189 r_symmetry_xyhbond_nbd_refined 0.183 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.172 r_nbd_other 0.158 r_symmetry_nbd_refined 0.151 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.083 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 1758 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing