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Mutant Streptomyces plicatus beta-hexosaminidase (D313N) in complex with product (GlcNAc)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HP4 PDB ENTRY 1HP4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 AMMONIUM SULPHATE, TRI-SODIUM CITRATE, SODIUM CHLORIDE, GLYCEROL, NAG, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 4.05 69.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.704 α = 90 b = 133.704 β = 90 c = 176.142 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV OSMIC optics 2001-08-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
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 1.95 40 96.9 0.056 30.5 19 65848 65848 -3 15.7
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) 1 1.95 2.02 98.5 0.256 5.5 19
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1HP4 1.95 39.19 65848 65848 6659 96.8 0.198 0.198 0.1933 0.218 0.2129 RANDOM 24.6
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] -0.07 0.76 -0.07 0.15
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.9 c_scangle_it 2.64 c_scbond_it 1.79 c_mcangle_it 1.68 c_angle_deg 1.3 c_mcbond_it 1.14 c_improper_angle_d 0.83 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.9 c_scangle_it 2.64 c_scbond_it 1.79 c_mcangle_it 1.68 c_angle_deg 1.3 c_mcbond_it 1.14 c_improper_angle_d 0.83 c_bond_d 0.005 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3864 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 29
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement CNS phasing