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Crystal structure of human histidine triad nucleotide-binding protein 1 (hHINT1) complexed with JB419 (AP4A analog)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TW2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 281 19% w/v PEG4000, 0.1 M sodium cacodylate pH 5.5
Crystal Properties Matthews coefficient Solvent content 3.03 59.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.714 α = 90 b = 46.419 β = 97.41 c = 103.413 γ = 90
Symmetry Space Group P 1 21 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 DECTRIS PILATUS 6M 2013-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.96690 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.34 102.55 97.6 0.096 7.1 3.3 25059 36.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.34 2.42 99 0.692 1.6 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3TW2 2.34 102.55 23826 1222 97.36 0.189 0.18642 0.1926 0.23907 0.24 RANDOM 60.124
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] 3.12 0.19 -4.22 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.924 r_dihedral_angle_3_deg 17.12 r_dihedral_angle_4_deg 15.623 r_long_range_B_refined 9.234 r_long_range_B_other 9.233 r_dihedral_angle_1_deg 6.899 r_scangle_other 4.33 r_mcangle_it 4.088 r_mcangle_other 4.087 r_scbond_it 2.567
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.924 r_dihedral_angle_3_deg 17.12 r_dihedral_angle_4_deg 15.623 r_long_range_B_refined 9.234 r_long_range_B_other 9.233 r_dihedral_angle_1_deg 6.899 r_scangle_other 4.33 r_mcangle_it 4.088 r_mcangle_other 4.087 r_scbond_it 2.567 r_scbond_other 2.567 r_mcbond_it 2.392 r_mcbond_other 2.392 r_angle_refined_deg 2.162 r_angle_other_deg 1.917 r_chiral_restr 0.135 r_bond_refined_d 0.023 r_gen_planes_refined 0.014 r_bond_other_d 0.013 r_gen_planes_other 0.01 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3495 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing