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Structure and activity of the GH20 beta-N-acetylhexosaminidase from Streptomyces coelicolor A3(2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4C7D PDB ENTRY 4C7D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1 M BIS-TRIS PH 6.5, 4 % (W/V) PEG 6000, 5 % DMSO
Crystal Properties Matthews coefficient Solvent content 3.3 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.79 α = 90 b = 129.24 β = 90 c = 149.94 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 120 2011-07-23 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 2 48.95 99.4 0.18 8.8 5.6 95616 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 2 2.1 98.6 0.53 3.2 5.7
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 4C7D 2 97.89 90731 4806 99.25 0.15848 0.15643 0.1571 0.19712 0.198 RANDOM 12.448
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] 0.5 0.28 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.42 r_dihedral_angle_4_deg 18.952 r_dihedral_angle_3_deg 12.562 r_dihedral_angle_1_deg 6.59 r_angle_refined_deg 1.855 r_scbond_it 1.462 r_mcangle_it 1.419 r_mcbond_it 0.904 r_chiral_restr 0.137 r_bond_refined_d 0.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.42 r_dihedral_angle_4_deg 18.952 r_dihedral_angle_3_deg 12.562 r_dihedral_angle_1_deg 6.59 r_angle_refined_deg 1.855 r_scbond_it 1.462 r_mcangle_it 1.419 r_mcbond_it 0.904 r_chiral_restr 0.137 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 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 r_mcangle_other 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 7655 Nucleic Acid Atoms Solvent Atoms 1147 Heterogen Atoms 160
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling