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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 ENTRY 5FQE
Crystallization Crystal Properties Matthews coefficient Solvent content 1.94 36.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.53 α = 90 b = 99.53 β = 90 c = 95.31 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 1.75 47.7 100 0.11 14.7 12.6 55369 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 1.75 1.78 100 0.48 2.6 8.2
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 ENTRY 5FQE 1.75 95.31 52619 2713 99.96 0.18274 0.18074 0.1884 0.22099 0.2247 RANDOM 35.234
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] 1.03 0.51 1.03 -3.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.94 r_dihedral_angle_4_deg 14.898 r_dihedral_angle_3_deg 13.882 r_dihedral_angle_1_deg 6.779 r_mcangle_it 3.692 r_scbond_it 3.248 r_mcbond_it 2.778 r_mcbond_other 2.778 r_angle_refined_deg 1.64 r_angle_other_deg 0.869
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.94 r_dihedral_angle_4_deg 14.898 r_dihedral_angle_3_deg 13.882 r_dihedral_angle_1_deg 6.779 r_mcangle_it 3.692 r_scbond_it 3.248 r_mcbond_it 2.778 r_mcbond_other 2.778 r_angle_refined_deg 1.64 r_angle_other_deg 0.869 r_chiral_restr 0.1 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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 4623 Nucleic Acid Atoms Solvent Atoms 415 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing