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Wildtype Streptomyces plicatus beta-hexosaminidase 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 SULFATE, TRI-SODIUM CITRATE, GLYCEROL, GlcNAc, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 4.02 69.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.276 α = 90 b = 133.276 β = 90 c = 176.204 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 MARRESEARCH 2000-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.979 SSRL BL9-1
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 2.1 70 99.8 0.038 39.4 12 54264 54264 -3 13.3
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 2.1 2.14 97.4 0.1 15.1 12 2604
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 2.1 70 54204 54204 5466 99.6 0.195 0.195 0.1877 0.216 0.2073 RANDOM 22
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] 1.99 0.91 1.99 -3.97
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 2.51 c_scbond_it 1.78 c_mcangle_it 1.64 c_angle_deg 1.3 c_mcbond_it 1.12 c_improper_angle_d 0.83 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3864 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms 41
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement CNS phasing