☰ Navigation Tabs
H33 variant of DoBi scaffold based on PIH1D1 N-terminal domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AVC 7AVC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 1 M (NH4)2SO4
1% (w/v) PEG3350
0.1 M Bis-Tris
Crystal Properties Matthews coefficient Solvent content 76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.131 α = 90 b = 123.131 β = 90 c = 190.106 γ = 90
Symmetry Space Group I 41 2 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 PIXEL DECTRIS PILATUS 6M 2019-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976260 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 2.47 47.53 69 0.126 0.136 0.036 0.999 14.8 12.6 18374
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 2.47 2.71 14.8 3.429 3.846 1.216 0.224 0.8 12.6
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-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 7AVC 2.471 47.53 18374 910 69.158 0.222 0.223 0.219 0.2235 0.255 0.2321 Random selection 81.639
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] 0.299 0.299 -0.599
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.435 r_lrange_other 19.356 r_lrange_it 19.353 r_dihedral_angle_6_deg 16.606 r_mcangle_other 14.056 r_mcangle_it 14.037 r_scangle_it 13.481 r_scangle_other 13.477 r_dihedral_angle_2_deg 10.028 r_mcbond_it 9.921
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.435 r_lrange_other 19.356 r_lrange_it 19.353 r_dihedral_angle_6_deg 16.606 r_mcangle_other 14.056 r_mcangle_it 14.037 r_scangle_it 13.481 r_scangle_other 13.477 r_dihedral_angle_2_deg 10.028 r_mcbond_it 9.921 r_mcbond_other 9.896 r_scbond_it 9.466 r_scbond_other 9.462 r_dihedral_angle_1_deg 6.366 r_angle_refined_deg 1.755 r_angle_other_deg 0.572 r_symmetry_xyhbond_nbd_refined 0.228 r_nbd_refined 0.218 r_symmetry_nbd_other 0.206 r_symmetry_nbd_refined 0.201 r_nbtor_refined 0.189 r_nbd_other 0.187 r_xyhbond_nbd_refined 0.115 r_symmetry_nbtor_other 0.093 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2071 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling PHASER phasing