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Crystal structure of human histidine triad nucleotide-binding protein 1 (hHINT1) crystallized at P212121 space group, and refined to 1.27 A
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 8.5 281 20% w/v PEG 3350, 0.1 M Bis-Tris Propane pH 8.5, 0.2 M Sodium/Potassium Phosphate
Crystal Properties Matthews coefficient Solvent content 2.58 52.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.031 α = 90 b = 76.364 β = 90 c = 80.864 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) 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 1.27 40.43 98.6 0.044 0.038 0.999 14.1 4.1 74711 8.4
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 1.27 1.29 95.8 0.535 0.461 0.775 3.8
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 1.27 40.43 70907 3746 98.36 0.10183 0.10022 0.1003 0.13326 0.1332 RANDOM 16.25
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] -0.25 0.25 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.464 r_sphericity_free 30.653 r_dihedral_angle_4_deg 13.63 r_dihedral_angle_3_deg 13.584 r_sphericity_bonded 11.757 r_rigid_bond_restr 7.016 r_dihedral_angle_1_deg 6.001 r_long_range_B_refined 4.812 r_long_range_B_other 4.811 r_scangle_other 4.457
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.464 r_sphericity_free 30.653 r_dihedral_angle_4_deg 13.63 r_dihedral_angle_3_deg 13.584 r_sphericity_bonded 11.757 r_rigid_bond_restr 7.016 r_dihedral_angle_1_deg 6.001 r_long_range_B_refined 4.812 r_long_range_B_other 4.811 r_scangle_other 4.457 r_scbond_it 3.851 r_scbond_other 3.85 r_angle_refined_deg 2.652 r_mcangle_it 2.473 r_mcangle_other 2.473 r_mcbond_it 1.836 r_mcbond_other 1.836 r_angle_other_deg 1.308 r_chiral_restr 0.163 r_bond_refined_d 0.03 r_gen_planes_refined 0.013 r_gen_planes_other 0.004 r_bond_other_d 0.002 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 1789 Nucleic Acid Atoms Solvent Atoms 414 Heterogen Atoms 27
Software Software Software Name Purpose MxCuBE data collection XDS data reduction Aimless data scaling MOLREP phasing REFMAC refinement