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Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - Gal-NHAc-DNJ complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.02M MgCl2, 0.1M HEPES-NaOH, 7.5% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.52 51.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.628 α = 90 b = 128.478 β = 90 c = 176.885 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 PIXEL DECTRIS PILATUS 2M-F 2016-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.1000 Photon Factory BL-1A
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 2.79 103.95 99.7 0.057 19.6 6.3 37110
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.79 2.85 100 0.518 0.979 2.4 6.7
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 SAD THROUGHOUT 2.79 103.95 35202 1852 98.66 0.23315 0.22899 0.2324 0.31325 0.3117 RANDOM 79.962
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 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.383 r_dihedral_angle_4_deg 18.17 r_dihedral_angle_3_deg 16.76 r_long_range_B_other 10.608 r_long_range_B_refined 10.607 r_dihedral_angle_1_deg 8.013 r_mcangle_it 7.72 r_mcangle_other 7.72 r_scangle_other 6.606 r_mcbond_it 4.863
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.383 r_dihedral_angle_4_deg 18.17 r_dihedral_angle_3_deg 16.76 r_long_range_B_other 10.608 r_long_range_B_refined 10.607 r_dihedral_angle_1_deg 8.013 r_mcangle_it 7.72 r_mcangle_other 7.72 r_scangle_other 6.606 r_mcbond_it 4.863 r_mcbond_other 4.855 r_scbond_it 4.027 r_scbond_other 4.027 r_angle_refined_deg 1.461 r_angle_other_deg 0.858 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_bond_other_d 0.006 r_gen_planes_refined 0.006 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9972 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing