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Structure of sucrose-6-phosphate hydrolase from Lactobacillus gasseri in complex with fructose
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 0.1 M buffer MMT pH 9.0; 25% (m/v) PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.47 50.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.86 α = 90 b = 103.86 β = 90 c = 102 γ = 90
Symmetry Space Group P 4 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 PIXEL DECTRIS PILATUS 2M 2014-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.4587 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 41.89 99.1 0.092 0.096 0.029 0.999 17 18 51784
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 88.2 0.272 0.345 0.209 0.895 2.7 4.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.8 41.89 49110 2643 99.05 0.13596 0.13438 0.16532 0.1647 RANDOM 12.947
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] -0.17 -0.17 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.104 r_dihedral_angle_4_deg 15.461 r_dihedral_angle_3_deg 12.292 r_dihedral_angle_1_deg 7.786 r_long_range_B_refined 4.898 r_long_range_B_other 4.684 r_scangle_other 3.043 r_scbond_it 1.929 r_scbond_other 1.928 r_angle_refined_deg 1.816
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.104 r_dihedral_angle_4_deg 15.461 r_dihedral_angle_3_deg 12.292 r_dihedral_angle_1_deg 7.786 r_long_range_B_refined 4.898 r_long_range_B_other 4.684 r_scangle_other 3.043 r_scbond_it 1.929 r_scbond_other 1.928 r_angle_refined_deg 1.816 r_mcangle_it 1.586 r_mcangle_other 1.586 r_angle_other_deg 1.552 r_mcbond_it 0.985 r_mcbond_other 0.985 r_chiral_restr 0.098 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3905 Nucleic Acid Atoms Solvent Atoms 497 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement TRUNCATE data reduction Aimless data scaling PHASER phasing