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Crystal structure of beta-hexosaminidase from Paenibacillus sp. TS12 in complex with NAG-thiazoline.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GH4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 Na-Acetate, PEG2000, (NH4)2SO4, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.29 46.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.696 α = 90 b = 102.094 β = 90 c = 108.06 γ = 90
Symmetry Space Group C 2 2 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 CCD MARMOSAIC 225 mm CCD 2009-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1 SPring-8 BL26B2
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 1.9 50 0.134 7.2 41603
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 1.9 1.93 0.425 4.8 1793
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 3GH4 1.9 50 39470 2106 99.03 0.14218 0.14013 0.1412 0.18061 0.1814 RANDOM 13.088
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] -0.49 0.7 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.57 r_dihedral_angle_4_deg 16.727 r_dihedral_angle_3_deg 13.304 r_dihedral_angle_1_deg 5.883 r_sphericity_free 3.952 r_scangle_it 2.969 r_sphericity_bonded 2.03 r_scbond_it 1.984 r_angle_refined_deg 1.365 r_mcangle_it 1.277
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.57 r_dihedral_angle_4_deg 16.727 r_dihedral_angle_3_deg 13.304 r_dihedral_angle_1_deg 5.883 r_sphericity_free 3.952 r_scangle_it 2.969 r_sphericity_bonded 2.03 r_scbond_it 1.984 r_angle_refined_deg 1.365 r_mcangle_it 1.277 r_rigid_bond_restr 1.26 r_mcbond_it 0.847 r_nbtor_refined 0.303 r_nbd_refined 0.187 r_symmetry_vdw_refined 0.179 r_symmetry_hbond_refined 0.173 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.105 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3909 Nucleic Acid Atoms Solvent Atoms 626 Heterogen Atoms 19
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling