☰ Navigation Tabs
Human histidine triad nucleotide-binding protein 2 (hHINT2) complexed with dGMP and refined to 2.77 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YQD 6YQD:B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 281 15 % (w/v) PEG6000, 5 % (v/v) glycerol
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.649 α = 90 b = 36.531 β = 103.034 c = 86.887 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 DECTRIS PILATUS 2M 2020-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
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 2.77 42.32 99.1 0.198 0.266 0.176 0.985 5.5 3.8 5698 31.4
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 2.77 2.92 99.1 0.668 0.894 0.589 0.799 2 3.9
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 6YQD:B 2.77 42.32 5695 565 98.649 0.218 0.2077 0.2144 0.3077 0.313 34.978
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] -1.837 1.086 5.134 -3.431
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.661 r_dihedral_angle_3_deg 19.373 r_dihedral_angle_4_deg 18.269 r_dihedral_angle_1_deg 6.486 r_lrange_it 4.975 r_lrange_other 4.973 r_mcangle_it 2.68 r_mcangle_other 2.679 r_scangle_other 2.411 r_scangle_it 2.409
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.661 r_dihedral_angle_3_deg 19.373 r_dihedral_angle_4_deg 18.269 r_dihedral_angle_1_deg 6.486 r_lrange_it 4.975 r_lrange_other 4.973 r_mcangle_it 2.68 r_mcangle_other 2.679 r_scangle_other 2.411 r_scangle_it 2.409 r_mcbond_other 1.577 r_mcbond_it 1.576 r_angle_refined_deg 1.491 r_scbond_it 1.376 r_scbond_other 1.373 r_angle_other_deg 1.139 r_xyhbond_nbd_refined 0.219 r_symmetry_nbd_other 0.213 r_nbd_refined 0.196 r_symmetry_xyhbond_nbd_refined 0.19 r_nbd_other 0.169 r_nbtor_refined 0.153 r_symmetry_nbd_refined 0.137 r_ncsr_local_group_1 0.126 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.065 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1756 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing