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Complex of XPB helicase with Bax1 endonuclease from Sulfurisphaera tokodaii at 3.15 Angstroms resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TNU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 0.1 M Tris-Cl, pH 8.0, 50 mM Sodium Carbonate, 32% PEG 400
Crystal Properties Matthews coefficient Solvent content 3.11 60.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 217.723 α = 90 b = 125.851 β = 101.52 c = 148.97 γ = 90
Symmetry Space Group C 1 2 1
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 ADSC QUANTUM 315 2015-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 12.3.1 1.0 ALS 12.3.1
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 3.15 145.969 85 0.144 0.161 0.072 6.6 4.5 57984
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 3.15 3.32 79.5 0.705 0.705 0.814 0.397 1.1 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 5TNU 3.15 29.93 55900 1999 84.85 0.2657 0.2651 0.2655 0.2824 0.2829 RANDOM 78.856
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] -1.18 0.09 -1.02 2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.253 r_dihedral_angle_4_deg 13.27 r_dihedral_angle_3_deg 13.232 r_dihedral_angle_1_deg 5.6 r_angle_refined_deg 1.328 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19961 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 21
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Coot model building MOSFLM data reduction