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beta-fructofuranosidase from Bifidobacterium longum - complex with fructose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PIG PDB ENTRY 3PIG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 293 0.4M ammonium chloride, 18% PEG 3350, 0.1M MES pH 7.0, protein concentration 11 mg/ml , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.06 40.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.765 α = 90 b = 86.765 β = 90 c = 223.868 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 225 mm CCD MIRRORS 2009-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 1.8 28.4 92.1 0.097 13.8 5.2 84167 -3
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 1.86 56 0.291 1.95 1.4
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 3PIG 1.8 28.4 84167 82477 1683 92.1 0.154 0.153 0.1642 0.208 0.2175 RANDOM 24.933
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] 0.37 0.18 0.37 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.268 r_dihedral_angle_4_deg 15.583 r_dihedral_angle_3_deg 13.669 r_dihedral_angle_1_deg 7.323 r_scangle_it 4.173 r_scbond_it 2.854 r_angle_refined_deg 1.727 r_mcangle_it 1.645 r_mcbond_it 1.023 r_chiral_restr 0.131
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.268 r_dihedral_angle_4_deg 15.583 r_dihedral_angle_3_deg 13.669 r_dihedral_angle_1_deg 7.323 r_scangle_it 4.173 r_scbond_it 2.854 r_angle_refined_deg 1.727 r_mcangle_it 1.645 r_mcbond_it 1.023 r_chiral_restr 0.131 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8295 Nucleic Acid Atoms Solvent Atoms 989 Heterogen Atoms 29
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing