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Crystal structure of a family 98 glycoside hydrolase catalytic module (Sp3GH98) in complex with the blood group A-trisaccharide (L19 mutant)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WMI PDB ENTRY 2WMI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 15% PEG 3350, 0.2M AMMONIUM SULFATE, 0.1M SODIUM ACETATE PH 4.8
Crystal Properties Matthews coefficient Solvent content 2.5 50.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.25 α = 90 b = 154.02 β = 90 c = 96.66 γ = 90
Symmetry Space Group C 2 2 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI CLSI 08B1-1
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 1.24 48.13 99.6 0.04 20.6 4.5 192579 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 1.24 1.31 98 0.31 4.7 3.9
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 2WMI 1.24 48.33 182768 9686 99.49 0.11764 0.11685 0.1257 0.13274 0.1391 RANDOM 9.731
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 0.01 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.028 r_dihedral_angle_4_deg 18.842 r_dihedral_angle_3_deg 11.004 r_dihedral_angle_1_deg 6.065 r_scangle_it 4.188 r_scbond_it 2.839 r_mcangle_it 1.896 r_angle_refined_deg 1.446 r_mcbond_it 1.195 r_rigid_bond_restr 1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.028 r_dihedral_angle_4_deg 18.842 r_dihedral_angle_3_deg 11.004 r_dihedral_angle_1_deg 6.065 r_scangle_it 4.188 r_scbond_it 2.839 r_mcangle_it 1.896 r_angle_refined_deg 1.446 r_mcbond_it 1.195 r_rigid_bond_restr 1.07 r_angle_other_deg 0.929 r_mcbond_other 0.39 r_chiral_restr 0.164 r_bond_refined_d 0.011 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_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4777 Nucleic Acid Atoms Solvent Atoms 1042 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling