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Human histidine triad nucleotide-binding protein 2 (hHINT2) refined to 1.26 A in H32 space group
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 7.5 281 0.8 M Na/K Tartrate, 0.1 M HEPES 7.5
Crystal Properties Matthews coefficient Solvent content 2.36 47.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.076 α = 90 b = 72.076 β = 90 c = 103.576 γ = 120
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-F 2016-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.0332 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.26 36.043 99.8 0.058 0.073 0.043 0.998 12.6 4.8 28102 9.5
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 1.26 1.28 99.8 0.645 0.815 0.492 0.685 2 4.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3TW2 1.26 36.043 28101 1375 99.73 0.118 0.1171 0.1174 0.1427 0.1443 13.669
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] -0.665 -0.333 -0.665 2.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.908 r_dihedral_angle_4_deg 17.379 r_dihedral_angle_3_deg 11.131 r_rigid_bond_restr 10.479 r_dihedral_angle_1_deg 6.33 r_lrange_it 4.609 r_scangle_it 3.856 r_scangle_other 3.854 r_lrange_other 3.816 r_scbond_it 3.354
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.908 r_dihedral_angle_4_deg 17.379 r_dihedral_angle_3_deg 11.131 r_rigid_bond_restr 10.479 r_dihedral_angle_1_deg 6.33 r_lrange_it 4.609 r_scangle_it 3.856 r_scangle_other 3.854 r_lrange_other 3.816 r_scbond_it 3.354 r_scbond_other 3.351 r_angle_refined_deg 2.077 r_mcangle_it 1.68 r_mcangle_other 1.679 r_angle_other_deg 1.611 r_mcbond_other 1.345 r_mcbond_it 1.342 r_symmetry_nbd_refined 0.906 r_symmetry_xyhbond_nbd_refined 0.403 r_nbd_refined 0.211 r_symmetry_nbd_other 0.208 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.166 r_nbd_other 0.162 r_chiral_restr 0.141 r_symmetry_nbtor_other 0.088 r_bond_refined_d 0.018 r_symmetry_xyhbond_nbd_other 0.015 r_gen_planes_refined 0.014 r_bond_other_d 0.01 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 756 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing