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XPB helicase in a complex with truncated Bax1 from Sulfurisphaera tokodaii at 2.96 Angstrom 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, SITTING DROP 7.5 298 200 mM Ammonium citrate, pH 7.5, 8% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.4 63.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.415 α = 83.09 b = 101.369 β = 81.15 c = 114.476 γ = 90.17
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 2018-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97741 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.95 50 99.1 0.098 0.116 0.061 5.8 3.5 51223
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 2.95 3 98.3 0.822 0.982 0.529 0.632 3.3
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 2.956 29.28 48672 2513 98.31 0.1855 0.183 0.183 0.2334 0.2333 RANDOM 77.683
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] -0.18 0.03 -0.04 0.15 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.043 r_dihedral_angle_4_deg 19.566 r_dihedral_angle_3_deg 17.045 r_dihedral_angle_1_deg 6.779 r_angle_refined_deg 1.593 r_chiral_restr 0.074 r_bond_refined_d 0.012 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12904 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction Coot model building HKL-2000 data reduction HKL-2000 data processing