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Human histidine triad nucleotide-binding protein 2 (hHINT2) refined to 1.65 A in P41212 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 298 20% (v/v) ethylene glycol, 5% (w/v) PEG 3350, 20 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.22 44.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.945 α = 90 b = 76.945 β = 90 c = 140.454 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-225 2014-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 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 1.65 46.82 100 0.077 0.084 0.035 0.999 15.3 10.8 51576 19.5
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 1.65 1.68 100 1.082 1.191 0.496 0.82 2.1 11
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 1.65 43.044 51490 2608 99.957 0.187 0.1845 0.1909 0.2331 0.2405 33.062
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] -1.569 -1.569 3.138
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.036 r_dihedral_angle_3_deg 14.41 r_dihedral_angle_4_deg 13.157 r_dihedral_angle_1_deg 7.189 r_lrange_it 6.112 r_lrange_other 6.022 r_scangle_it 4.387 r_scangle_other 4.387 r_mcangle_it 3.703 r_mcangle_other 3.703
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.036 r_dihedral_angle_3_deg 14.41 r_dihedral_angle_4_deg 13.157 r_dihedral_angle_1_deg 7.189 r_lrange_it 6.112 r_lrange_other 6.022 r_scangle_it 4.387 r_scangle_other 4.387 r_mcangle_it 3.703 r_mcangle_other 3.703 r_scbond_it 2.947 r_scbond_other 2.947 r_mcbond_other 2.758 r_mcbond_it 2.757 r_angle_refined_deg 1.586 r_angle_other_deg 1.33 r_metal_ion_refined 0.353 r_symmetry_nbd_refined 0.257 r_symmetry_metal_ion_refined 0.242 r_nbd_other 0.226 r_xyhbond_nbd_refined 0.205 r_nbd_refined 0.2 r_symmetry_nbd_other 0.184 r_symmetry_xyhbond_nbd_refined 0.176 r_nbtor_refined 0.154 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_other 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3308 Nucleic Acid Atoms Solvent Atoms 381 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing