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Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - ligand free
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 = 63.637 α = 90 b = 127.764 β = 90 c = 176.756 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 CCD ADSC QUANTUM 210 2015-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 2.64 103.55 99.6 0.086 18.3 6.9 42830
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 2.65 2.7 99.2 0.627 0.849 1.9 6.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.64 103.55 40656 2114 99.07 0.23453 0.23053 0.31098 0.281 RANDOM 65.353
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] 0.12 -0.05 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.209 r_dihedral_angle_3_deg 20.185 r_dihedral_angle_4_deg 17.214 r_long_range_B_refined 9.77 r_dihedral_angle_1_deg 7.704 r_mcangle_it 6.404 r_scbond_it 4.258 r_mcbond_it 4.187 r_angle_refined_deg 1.713 r_chiral_restr 0.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.209 r_dihedral_angle_3_deg 20.185 r_dihedral_angle_4_deg 17.214 r_long_range_B_refined 9.77 r_dihedral_angle_1_deg 7.704 r_mcangle_it 6.404 r_scbond_it 4.258 r_mcbond_it 4.187 r_angle_refined_deg 1.713 r_chiral_restr 0.111 r_bond_refined_d 0.037 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 9587 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing