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Crystal structure of the fructose specific IIB subunit of PTS system from Bacillus subtilis subsp. subtilis str. 168
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 0.2 M Sodium citrate tribasic dihydrate, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.78 30.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.931 α = 90 b = 48.931 β = 90 c = 68.25 γ = 90
Symmetry Space Group P 41 21 2
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 ADSC QUANTUM 315 mirrors 2007-08-03 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97950, 0.97960 APS 19-ID
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 1.8 40 95 0.07 28.7 7 7790 7790
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 1.8 1.85 61.7 0.378 3.3 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.8 39.78 7785 7402 361 95.19 0.1871 0.18601 0.18328 0.1911 0.23743 0.2439 RANDOM 17.628
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] 1.57 1.57 -3.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.292 r_dihedral_angle_4_deg 14.832 r_dihedral_angle_3_deg 13.805 r_dihedral_angle_1_deg 5.461 r_scangle_it 3.519 r_scbond_it 2.453 r_angle_refined_deg 1.712 r_mcangle_it 1.417 r_mcbond_it 1.171 r_angle_other_deg 1.033
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.292 r_dihedral_angle_4_deg 14.832 r_dihedral_angle_3_deg 13.805 r_dihedral_angle_1_deg 5.461 r_scangle_it 3.519 r_scbond_it 2.453 r_angle_refined_deg 1.712 r_mcangle_it 1.417 r_mcbond_it 1.171 r_angle_other_deg 1.033 r_mcbond_other 0.267 r_symmetry_vdw_other 0.248 r_symmetry_vdw_refined 0.229 r_nbd_other 0.207 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.201 r_nbtor_refined 0.171 r_symmetry_hbond_refined 0.135 r_chiral_restr 0.092 r_nbtor_other 0.089 r_bond_refined_d 0.019 r_bond_other_d 0.011 r_gen_planes_refined 0.006 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 795 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing SHELXD phasing SHELXE model building MLPHARE phasing DM phasing SOLVE phasing RESOLVE phasing ARP/wARP model building CCP4 phasing Coot model building