☰ Navigation Tabs
Structure of endo-beta-N-acetylglucosaminidase HS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SAD-derived and unpublished
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 2.0M Ammonium sulfate, 0.1M Bis-Tris-HCl buffer
Crystal Properties Matthews coefficient Solvent content 2.6 52.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.927 α = 90 b = 135.567 β = 90 c = 238.865 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 Collimating mirror (19.2 m): Rhodium coated silicon single crystal (Flat shaped, 1000 mm (L) x 80 mm (W) x 70 mm (T)) with 3.5 mrad glancing angle Monochromator (20.8 m): Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling Focusing mirror (22.9 m): Rhodium coated SiO2 (Troidal, 1000 mm (L) x 100 mm (W) x 65 mm (T)) with 3.5 mrad glancing angle 2023-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.00 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.8 49.7 99.8 0.085 0.093 0.036 0.999 12.9 6.6 212496 21.21
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.81 1.84 96.4 0.686 0.748 0.292 0.896 2.8 6.3
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.81 39.05 1.34 212226 10601 99.8 0.1981 0.1959 0.1961 0.2421 0.2421 27.43
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.6351 f_angle_d 0.8805 f_chiral_restr 0.0555 f_plane_restr 0.0071 f_bond_d 0.0067
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15044 Nucleic Acid Atoms Solvent Atoms 2377 Heterogen Atoms 42
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling Coot model building MOLREP phasing