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Human TOP3B-TDRD3 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GVC 5GVC, 5GVD experimental model PDB 5GVD 5GVC, 5GVD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 293 50 mM Na-cacodylate, 10 mM MgSO4, 1.7 M Li2SO4
Crystal Properties Matthews coefficient Solvent content 5.59 78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.563 α = 90 b = 173.563 β = 90 c = 111.81 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 CMOS DECTRIS PILATUS3 S 6M 2015-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.6 50 99.9 11.2 9 22224
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.6 3.66
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5GVC, 5GVD 3.606 46.997 1.41 22208 1134 99.88 0.2004 0.1981 0.2049 0.2452 0.2495
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.516 f_angle_d 1.135 f_chiral_restr 0.079 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6082 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing