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DoBi scaffold based on PIH1D1 N-terminal domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PSF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 10% glycerol, 4M sodium formate
Crystal Properties Matthews coefficient Solvent content 2.88 57.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.723 α = 90 b = 72.723 β = 90 c = 192.775 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 2016-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
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 1.2 38.27 97.1 0.247 0.261 0.083 0.978 5.4 9.6 59704 11.7
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 1.2 1.22 74.4 1.215 1.32 0.5 0.498 1.3 6.4
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4PSF 1.2 38.27 59703 3028 96.869 0.173 0.13984 0.13611 0.1724 0.15419 0.179 19.703
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] 0.148 0.074 0.148 -0.479
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.651 r_dihedral_angle_4_deg 25.033 r_dihedral_angle_3_deg 13.32 r_lrange_it 6.827 r_lrange_other 6.5 r_dihedral_angle_1_deg 6.092 r_scangle_it 5.4 r_scangle_other 5.397 r_scbond_it 3.915 r_scbond_other 3.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.651 r_dihedral_angle_4_deg 25.033 r_dihedral_angle_3_deg 13.32 r_lrange_it 6.827 r_lrange_other 6.5 r_dihedral_angle_1_deg 6.092 r_scangle_it 5.4 r_scangle_other 5.397 r_scbond_it 3.915 r_scbond_other 3.912 r_mcangle_it 3.514 r_mcangle_other 3.512 r_mcbond_it 2.352 r_mcbond_other 2.339 r_angle_other_deg 2.335 r_angle_refined_deg 1.921 r_symmetry_nbd_refined 0.249 r_nbd_other 0.243 r_nbd_refined 0.231 r_symmetry_xyhbond_nbd_refined 0.217 r_symmetry_nbd_other 0.21 r_xyhbond_nbd_refined 0.209 r_nbtor_refined 0.182 r_symmetry_metal_ion_refined 0.146 r_chiral_restr 0.113 r_symmetry_nbtor_other 0.083 r_metal_ion_refined 0.08 r_bond_other_d 0.034 r_gen_planes_other 0.031 r_bond_refined_d 0.017 r_gen_planes_refined 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1132 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing