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Structure of endo-beta-N-acetylglucosaminidase A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 289 14% (w/v) PEG 8000, 160mM calcium acetate, 20% (v/v) glycerol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.35 47.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.892 α = 84.23 b = 78.972 β = 80.77 c = 117.267 γ = 64.01
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 273 IMAGE PLATE RIGAKU RAXIS IV++ M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 20 67.9 3.8 171567 116494 2 2 21.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 67.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 20 2 110656 5824 0.20539 0.20539 0.20297 0.2128 0.25143 0.2559 RANDOM 22.042
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] -0.77 -0.38 1.38 1.13 -0.01 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.805 r_dihedral_angle_3_deg 14.668 r_dihedral_angle_4_deg 13.02 r_dihedral_angle_1_deg 5.968 r_scangle_it 4.176 r_rigid_bond_restr 3.94 r_scbond_it 3.865 r_mcangle_it 1.797 r_sphericity_bonded 1.645 r_sphericity_free 1.281
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.805 r_dihedral_angle_3_deg 14.668 r_dihedral_angle_4_deg 13.02 r_dihedral_angle_1_deg 5.968 r_scangle_it 4.176 r_rigid_bond_restr 3.94 r_scbond_it 3.865 r_mcangle_it 1.797 r_sphericity_bonded 1.645 r_sphericity_free 1.281 r_angle_refined_deg 1.027 r_mcbond_it 0.977 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18703 Nucleic Acid Atoms Solvent Atoms 2171 Heterogen Atoms 22
Software Software Software Name Purpose HKL-2000 data collection OASIS model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling OASIS phasing