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S. tokodaii XPB II crystal structure at 3.0 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FWR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 1:1 ratio of protein with 10 mM sodium citrate pH 5.6, 1770 mM ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.9 68.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.922 α = 90 b = 160.922 β = 90 c = 122.96 γ = 90
Symmetry Space Group P 43 21 2
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 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 3.05 29.88 99.9 0.374 0.382 0.078 0.996 11.2 23.6 31341
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 3.05 3.21 100 2.904 2.967 0.609 0.629 23.4
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 (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 2FWR 3.05 29.88 29713 1562 99.8 0.1976 0.1961 0.201 0.226 0.2339 RANDOM 90.199
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] 2.1 2.1 -4.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.617 r_dihedral_angle_3_deg 20.25 r_dihedral_angle_4_deg 15.318 r_dihedral_angle_1_deg 7.355 r_angle_refined_deg 1.312 r_angle_other_deg 0.817 r_chiral_restr 0.074 r_gen_planes_refined 0.012 r_bond_refined_d 0.01 r_gen_planes_other 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.617 r_dihedral_angle_3_deg 20.25 r_dihedral_angle_4_deg 15.318 r_dihedral_angle_1_deg 7.355 r_angle_refined_deg 1.312 r_angle_other_deg 0.817 r_chiral_restr 0.074 r_gen_planes_refined 0.012 r_bond_refined_d 0.01 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6398 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 109
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing DM phasing PDB_EXTRACT data extraction Coot model building