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GH20C, Beta-hexosaminidase from Streptococcus pneumoniae in complex with PUGNAc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EPN PDB ENTRY 2EPN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 10.2 12% (W/V) PEG 3350, 0.2 M MAGNESIUM CHLORIDE, 0.05 M CAPS, PH 10.2, 1% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.25 45.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.699 α = 90 b = 136.937 β = 90 c = 201.446 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 291 CCD MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.78 38.66 99.6 0.04 28.2 7.8 248507 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.81 93.2 0.33 3.9 4.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2EPN 1.77 38.69 235893 12474 99.62 0.16596 0.16402 0.175 0.20266 0.2105 RANDOM 24.607
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] 2.33 -1.7 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.21 r_dihedral_angle_4_deg 15.909 r_dihedral_angle_3_deg 12.506 r_dihedral_angle_1_deg 6.544 r_angle_refined_deg 1.828 r_angle_other_deg 0.926 r_chiral_restr 0.122 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.21 r_dihedral_angle_4_deg 15.909 r_dihedral_angle_3_deg 12.506 r_dihedral_angle_1_deg 6.544 r_angle_refined_deg 1.828 r_angle_other_deg 0.926 r_chiral_restr 0.122 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19325 Nucleic Acid Atoms Solvent Atoms 1958 Heterogen Atoms 103
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing