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Crystal structure of a family 98 glycoside hydrolase catalytic module (Sp3GH98) in complex with the blood group A-trisaccharide (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 TRIHYDRATE PH 4.8
Crystal Properties Matthews coefficient Solvent content 2.5 50.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.35 α = 90 b = 154.3 β = 90 c = 96.7 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 CCD MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 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 1.52 48.13 100 0.14 10.1 7.4 105928 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 1.52 1.6 100 0.49 4.1 7.4
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 1.52 48.35 100587 5290 99.93 0.1279 0.12642 0.1379 0.15601 0.1653 RANDOM 9.464
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] 0.02 0.07 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.989 r_dihedral_angle_4_deg 18.45 r_dihedral_angle_3_deg 11.655 r_dihedral_angle_1_deg 5.612 r_scangle_it 3.697 r_scbond_it 2.484 r_angle_refined_deg 1.615 r_mcangle_it 1.521 r_angle_other_deg 1.068 r_rigid_bond_restr 0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.989 r_dihedral_angle_4_deg 18.45 r_dihedral_angle_3_deg 11.655 r_dihedral_angle_1_deg 5.612 r_scangle_it 3.697 r_scbond_it 2.484 r_angle_refined_deg 1.615 r_mcangle_it 1.521 r_angle_other_deg 1.068 r_rigid_bond_restr 0.99 r_mcbond_it 0.953 r_mcbond_other 0.345 r_chiral_restr 0.161 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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_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 4770 Nucleic Acid Atoms Solvent Atoms 989 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling