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Crystal structure of a bacteria TIR domain, PdTIR from Paracoccus denitrificans
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 0.1 M sodium cacodylate pH 6.0, 31% PEG 8000 and 0.2 M ammonium sulfate , VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.27 45.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.78 α = 90 b = 85.61 β = 90 c = 89.62 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 98 2008-05-20 M MAD 2 1 x-ray 98 2008-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.979, 0.980, 0.855 SSRL BL9-2 2 SYNCHROTRON SSRL BEAMLINE BL9-2 0.979 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1,2 2.5 50 95.4 0.06 23.711 3.9 20938
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.59 78.8 0.192 3.5
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 MAD 2.5 8 1684 21351 17535 1725 82.1 0.192 0.192 0.2095 0.243 0.2587 40.611
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] 23.597 -12.203 -11.394
RMS Deviations Key Refinement Restraint Deviation c_angle_d 1.237 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d_na c_angle_d_prot c_angle_deg c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d
RMS Deviations Key Refinement Restraint Deviation c_angle_d 1.237 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d_na c_angle_d_prot c_angle_deg c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4229 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 5
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement PDB_EXTRACT data extraction HKL-2000 data collection SOLVE phasing