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Crystal structure of endo-alpha-N-acetylgalactosaminidase from Bifidobacterium longum (EngBF)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 293 0.1M MES-NaOH, 3% PEG 20000, 25% MPD, 0.2M NaCl, 0.01M MnCl2, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.38 71.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 192.267 α = 90 b = 192.267 β = 90 c = 123.017 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 100 CCD ADSC QUANTUM 4 2008-02-17 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 0.96787, 0.97923, 0.97939, 0.96416 Photon Factory BL-6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 50 99.1 0.075 27.2 7.2 174089 172447 27.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.07 99.8 0.467 3.5 6.5 17314
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 MAD THROUGHOUT 2 36.49 172447 163203 8598 98.71 0.17324 0.17203 0.1731 0.19564 0.1975 RANDOM 30.743
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] 0.03 0.01 0.03 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.216 r_dihedral_angle_4_deg 16.375 r_dihedral_angle_3_deg 13.409 r_dihedral_angle_1_deg 6.655 r_scangle_it 3.285 r_scbond_it 2.14 r_angle_refined_deg 1.408 r_mcangle_it 1.362 r_mcbond_it 0.842 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.216 r_dihedral_angle_4_deg 16.375 r_dihedral_angle_3_deg 13.409 r_dihedral_angle_1_deg 6.655 r_scangle_it 3.285 r_scbond_it 2.14 r_angle_refined_deg 1.408 r_mcangle_it 1.362 r_mcbond_it 0.842 r_nbtor_refined 0.304 r_nbd_refined 0.196 r_symmetry_vdw_refined 0.179 r_symmetry_hbond_refined 0.134 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9070 Nucleic Acid Atoms Solvent Atoms 1427 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling SOLVE phasing