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Family 89 Glycoside Hydrolase from Clostridium perfringens in complex with 2-acetamido-1,2-dideoxynojirmycin
Crystallization Crystal Properties Matthews coefficient Solvent content 2.84 56.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.96 α = 90 b = 90.96 β = 90 c = 252.4 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 113.15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE
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 2.36 19.83 90.7 0.13 3.27 42780 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 OTHER THROUGHOUT NONE 2.36 19.7 41573 2198 90.7 0.205 0.203 0.1988 0.246 0.2384 RANDOM 34.49
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] 1.06 0.53 1.06 -1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.909 r_dihedral_angle_4_deg 18.012 r_dihedral_angle_3_deg 15.575 r_dihedral_angle_1_deg 5.915 r_scangle_it 1.759 r_angle_refined_deg 1.157 r_scbond_it 1.084 r_mcangle_it 0.702 r_mcbond_it 0.373 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.909 r_dihedral_angle_4_deg 18.012 r_dihedral_angle_3_deg 15.575 r_dihedral_angle_1_deg 5.915 r_scangle_it 1.759 r_angle_refined_deg 1.157 r_scbond_it 1.084 r_mcangle_it 0.702 r_mcbond_it 0.373 r_nbtor_refined 0.305 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.193 r_xyhbond_nbd_refined 0.155 r_symmetry_hbond_refined 0.096 r_chiral_restr 0.084 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other 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 7151 Nucleic Acid Atoms Solvent Atoms 381 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement