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Crystal structure of Putative TOXIN related protein (YP_001303978.1) from Parabacteroides distasonis ATCC 8503 at 2.16 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.79 277 5.0000% polyethylene glycol 3000, 44.0000% polyethylene glycol 400, 0.1M MES pH 5.79, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.722 α = 90 b = 71.722 β = 90 c = 102.566 γ = 120
Symmetry Space Group P 31 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 MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2009-07-31 M MAD 2 1 x-ray 100 CCD MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2009-02-23 M MAD ,0.91162 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97911 SSRL BL9-2 2 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97835,0.97876 SSRL BL11-1 ,0.91162
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 2.16 39.559 99.4 0.032 19.28 16892 -3 52.236
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) 1,2 2.16 2.24 99.5 0.688 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.16 39.559 16861 853 99.85 0.205 0.203 0.2202 0.235 0.2521 RANDOM 50.118
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] -1.48 -0.74 -1.48 2.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.016 r_dihedral_angle_4_deg 17.405 r_dihedral_angle_3_deg 15.148 r_dihedral_angle_1_deg 6.504 r_scangle_it 3.529 r_scbond_it 2.241 r_mcangle_it 1.678 r_angle_refined_deg 1.596 r_mcbond_it 0.922 r_angle_other_deg 0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.016 r_dihedral_angle_4_deg 17.405 r_dihedral_angle_3_deg 15.148 r_dihedral_angle_1_deg 6.504 r_scangle_it 3.529 r_scbond_it 2.241 r_mcangle_it 1.678 r_angle_refined_deg 1.596 r_mcbond_it 0.922 r_angle_other_deg 0.85 r_mcbond_other 0.21 r_chiral_restr 0.098 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1580 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement PHENIX refinement MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHARP phasing autoSHARP phasing