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Crystal structure of a family 98 glycoside hydrolase catalytic module (Sp3GH98) in complex with the type 1 blood group A-tetrasaccharide (E558A X02 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 2.52 51.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.26 α = 90 b = 154.75 β = 90 c = 97.16 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 IMAGE PLATE RIGAKU R-AXIS 4 OSMIC BLUE M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-002
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 1.65 30.7 99.9 0.07 14.2 3.8 83578 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 1.65 1.74 99.3 0.5 2.2 3.4
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 1.65 30.16 79310 4167 99.88 0.14743 0.14541 0.1541 0.18564 0.1891 RANDOM 11.256
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 0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.964 r_dihedral_angle_4_deg 17.715 r_dihedral_angle_3_deg 12.016 r_dihedral_angle_1_deg 6.006 r_scangle_it 3.875 r_scbond_it 2.59 r_mcangle_it 1.52 r_angle_refined_deg 1.294 r_rigid_bond_restr 1.026 r_mcbond_it 0.916
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.964 r_dihedral_angle_4_deg 17.715 r_dihedral_angle_3_deg 12.016 r_dihedral_angle_1_deg 6.006 r_scangle_it 3.875 r_scbond_it 2.59 r_mcangle_it 1.52 r_angle_refined_deg 1.294 r_rigid_bond_restr 1.026 r_mcbond_it 0.916 r_angle_other_deg 0.874 r_mcbond_other 0.264 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 4775 Nucleic Acid Atoms Solvent Atoms 819 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling