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Crystal structure of a putative outer membrane protein (BF2706) from Bacteroides fragilis NCTC 9343 at 2.40 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 0.2M potassium sodium tartrate, 2.0M ammonium sulfate, 0.1M sodium citrate pH 5.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.81 74.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.154 α = 90 b = 154.154 β = 90 c = 40.164 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 Vertical focusing mirror; double crystal Si(111) monochromator 2011-03-25 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 0.96109,0.97934,0.97908 SSRL BL14-1
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 2.4 29.816 98.4 0.09 10.91 21589 -3 48.034
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 2.4 2.49 96.7 0.672 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 2.4 29.816 21577 1107 99.78 0.2006 0.1984 0.1907 0.2418 0.2266 RANDOM 33.2552
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] 1.09 0.54 1.09 -1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.691 r_dihedral_angle_3_deg 13.986 r_dihedral_angle_4_deg 9.802 r_dihedral_angle_1_deg 5.967 r_scangle_it 3.924 r_scbond_it 2.266 r_angle_refined_deg 1.518 r_mcangle_it 1.316 r_angle_other_deg 0.83 r_mcbond_it 0.638
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.691 r_dihedral_angle_3_deg 13.986 r_dihedral_angle_4_deg 9.802 r_dihedral_angle_1_deg 5.967 r_scangle_it 3.924 r_scbond_it 2.266 r_angle_refined_deg 1.518 r_mcangle_it 1.316 r_angle_other_deg 0.83 r_mcbond_it 0.638 r_mcbond_other 0.119 r_chiral_restr 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1928 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 52
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction SHELX phasing SHARP phasing XSCALE data scaling REFMAC refinement XDS data reduction SHELXD phasing