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1.85 Angstrom Resolution Crystal Structure of PTS System Cellobiose-specific Transporter Subunit IIB from Bacillus anthracis.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IIB PDB ENTRY 1IIB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 295 Protein: 7.5 mG/mL, 0.25 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3;
Screen: Classics II (B7), 0.056 M Sodium phosphate, 1.344 M Potasium phosphate;
Cryo: 4.0 M Sodium formate., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.77 30.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.788 α = 90 b = 70.802 β = 90 c = 84.464 γ = 90
Symmetry Space Group C 2 2 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 300 mm CCD Beryllium lenses 2013-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 1.85 30 99.6 0.049 33.5 7.1 15627 15627 -3 36.9
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 1.85 1.88 98.1 0.502 3.2 5.9 736
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 1IIB 1.85 29.89 14797 14797 777 99.58 0.17841 0.17841 0.17608 0.1856 0.22364 0.228 RANDOM 56.509
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] -2.93 -0.41 3.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.7 r_dihedral_angle_4_deg 13.66 r_dihedral_angle_3_deg 12.01 r_long_range_B_other 9.159 r_long_range_B_refined 9.149 r_scangle_other 6.167 r_scbond_it 4.242 r_scbond_other 4.223 r_mcangle_it 3.906 r_mcangle_other 3.904
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.7 r_dihedral_angle_4_deg 13.66 r_dihedral_angle_3_deg 12.01 r_long_range_B_other 9.159 r_long_range_B_refined 9.149 r_scangle_other 6.167 r_scbond_it 4.242 r_scbond_other 4.223 r_mcangle_it 3.906 r_mcangle_other 3.904 r_dihedral_angle_1_deg 2.971 r_mcbond_it 2.87 r_mcbond_other 2.865 r_angle_refined_deg 1.472 r_angle_other_deg 0.761 r_chiral_restr 0.095 r_bond_refined_d 0.012 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 1616 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 5
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling