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The details of glycolipid glycan hydrolysis by the structural analysis of a family 123 glycoside hydrolase from Clostridium perfringens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FQE PDB ENTR 5FQE
Crystallization Crystal Properties Matthews coefficient Solvent content 2.43 49.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.13 α = 90 b = 111.13 β = 90 c = 95.77 γ = 120
Symmetry Space Group P 32 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 MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 CLSI 08ID-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 2.1 48.1 99.5 0.09 15.2 10.8 39970 2
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 2.1 2.16 99.2 0.73 2.9 11
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTR 5FQE 2.1 96.24 38008 1962 99.35 0.18354 0.18058 0.1874 0.24058 0.241 RANDOM 46.214
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] 0.92 0.46 0.92 -2.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.114 r_dihedral_angle_4_deg 16.201 r_dihedral_angle_3_deg 14.012 r_dihedral_angle_1_deg 6.568 r_mcangle_it 4.167 r_scbond_it 3.655 r_mcbond_it 2.942 r_mcbond_other 2.929 r_angle_refined_deg 1.475 r_angle_other_deg 0.759
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.114 r_dihedral_angle_4_deg 16.201 r_dihedral_angle_3_deg 14.012 r_dihedral_angle_1_deg 6.568 r_mcangle_it 4.167 r_scbond_it 3.655 r_mcbond_it 2.942 r_mcbond_other 2.929 r_angle_refined_deg 1.475 r_angle_other_deg 0.759 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4693 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing