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Structure of human POLDIP2, a multifaceted adaptor protein in metabolism and genome stability
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VBV 1VBV, 5HDW experimental model PDB 5HDW 1VBV, 5HDW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M Calcium acetate hydrate
0.1M Sodium cacodylate
pH 6.5
40% (v/v) PEG 300
Crystal Properties Matthews coefficient Solvent content 2.79 56.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.138 α = 90 b = 120.138 β = 90 c = 49.516 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 110 PIXEL Bruker PHOTON II Microfocus Source 2019-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER IMUS MICROFOCUS 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.687 104.042 99.6 0.147 0.159 0.058 13.2 7.1 11561 45.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.69 2.83 98.7 2.049 2.049 2.397 1.216 0.4 3.7
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 (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 1VBV, 5HDW 2.8 23.88 9711 524 99.67 0.2199 0.2163 0.2206 0.2881 0.2909 RANDOM 42.602
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] -0.2 -0.1 -0.2 0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.173 r_dihedral_angle_3_deg 22.487 r_dihedral_angle_4_deg 22.133 r_dihedral_angle_1_deg 9.06 r_angle_refined_deg 1.608 r_angle_other_deg 1.178 r_chiral_restr 0.062 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.173 r_dihedral_angle_3_deg 22.487 r_dihedral_angle_4_deg 22.133 r_dihedral_angle_1_deg 9.06 r_angle_refined_deg 1.608 r_angle_other_deg 1.178 r_chiral_restr 0.062 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2130 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 1
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction PROTEUM2 data reduction