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The details of glycolipid glycan hydrolysis by the structural analysis of a family 123 glycoside hydrolase from Clostridium perfringens
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.20 M SODIUM FORMATE, 11% (W/V) POLYETHYLENE GLYCOL 3350, AND 0.1 M HEPES, PH 7
Crystal Properties Matthews coefficient Solvent content 2.48 50.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.42 α = 90 b = 115.03 β = 90 c = 135.58 γ = 90
Symmetry Space Group P 21 21 21
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 1.5 87.7 98.8 0.05 16.2 4.9 209500 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 1.5 1.54 99.4 0.41 2.6 3.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.53 87.71 188180 9845 98.49 0.15948 0.15813 0.1685 0.18515 0.1925 RANDOM 16.476
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.293 r_dihedral_angle_4_deg 12.107 r_dihedral_angle_3_deg 11.751 r_dihedral_angle_1_deg 6.321 r_scbond_it 2.153 r_mcangle_it 1.923 r_angle_refined_deg 1.726 r_mcbond_other 1.31 r_mcbond_it 1.309 r_angle_other_deg 1.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.293 r_dihedral_angle_4_deg 12.107 r_dihedral_angle_3_deg 11.751 r_dihedral_angle_1_deg 6.321 r_scbond_it 2.153 r_mcangle_it 1.923 r_angle_refined_deg 1.726 r_mcbond_other 1.31 r_mcbond_it 1.309 r_angle_other_deg 1.017 r_chiral_restr 0.112 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 9402 Nucleic Acid Atoms Solvent Atoms 1277 Heterogen Atoms 153
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing