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Crystal structure of Putative pore-forming toxin (YP_001301288.1) from Bacteroides vulgatus ATCC 8482 at 1.85 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.43 293 31.6000% 2-methyl-2,4-pentanediol, 0.2000M sodium chloride, 0.1M sodium acetate pH 4.43, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 44.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.796 α = 90 b = 70.337 β = 90 c = 104.1 γ = 90
Symmetry Space Group I 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 100 CCD MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2009-06-10 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.85503,0.97926,0.97845 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.85 29.814 100 0.091 0.091 10.2 4.1 21313 21.528
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.9 100 0.726 0.726 1 4.1 1549
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 1.85 29.814 21310 1095 99.99 0.184 0.182 0.1944 0.214 0.2256 RANDOM 18.402
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] -0.25 -0.07 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.549 r_dihedral_angle_4_deg 17.383 r_dihedral_angle_3_deg 14.076 r_dihedral_angle_1_deg 6.642 r_scangle_it 4.3 r_scbond_it 2.69 r_mcangle_it 1.697 r_angle_refined_deg 1.621 r_mcbond_it 0.959 r_angle_other_deg 0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.549 r_dihedral_angle_4_deg 17.383 r_dihedral_angle_3_deg 14.076 r_dihedral_angle_1_deg 6.642 r_scangle_it 4.3 r_scbond_it 2.69 r_mcangle_it 1.697 r_angle_refined_deg 1.621 r_mcbond_it 0.959 r_angle_other_deg 0.93 r_mcbond_other 0.277 r_chiral_restr 0.102 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1729 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SOLVE phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction