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Crystal structure of human histidine triad nucleotide-binding protein 1 (hHINT1) crystallized at P212121 space group, with visible extended fragment of N-terminus
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 7 281 25% PEG 1500, 0.1 M MMT Buffer pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.55 51.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.075 α = 90 b = 63.379 β = 90 c = 76.836 γ = 90
Symmetry Space Group P 21 21 21
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 2016-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918409 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.43 39.52 96.1 0.137 0.161 0.994 8.78 3.77 40954 15
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.43 1.51 92.7 0.703 0.821 0.833 1.96 3.74
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 1.43 39.52 38759 2041 95.82 0.2263 0.22362 0.2237 0.27726 0.2793 RANDOM 9.995
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] -0.73 0.29 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.442 r_sphericity_free 30.801 r_dihedral_angle_4_deg 15.412 r_dihedral_angle_3_deg 14.09 r_sphericity_bonded 12.113 r_dihedral_angle_1_deg 6.676 r_long_range_B_refined 4.388 r_long_range_B_other 3.698 r_rigid_bond_restr 3.457 r_scangle_other 2.559
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.442 r_sphericity_free 30.801 r_dihedral_angle_4_deg 15.412 r_dihedral_angle_3_deg 14.09 r_sphericity_bonded 12.113 r_dihedral_angle_1_deg 6.676 r_long_range_B_refined 4.388 r_long_range_B_other 3.698 r_rigid_bond_restr 3.457 r_scangle_other 2.559 r_mcangle_it 2.323 r_mcangle_other 2.323 r_mcbond_it 2.118 r_mcbond_other 2.117 r_scbond_other 1.928 r_scbond_it 1.927 r_angle_refined_deg 1.812 r_angle_other_deg 0.61 r_chiral_restr 0.096 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1841 Nucleic Acid Atoms Solvent Atoms 401 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing