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Crystal structure of beta-hexosaminidase from Paenibacillus sp. TS12 in complex with GalNAc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HP4 PDB 1HP4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 Na-Acetate, PEG2000, 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 = 95.667 α = 90 b = 102.123 β = 90 c = 108.074 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 CCD ADSC QUANTUM 315 2007-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
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 97.9 0.117 12.2 4.4 41113
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 91.5 0.254 3.4 2.9
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 1HP4 1.9 34.91 39027 2071 97.88 0.14181 0.13978 0.1404 0.18004 0.1799 RANDOM 9.92
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] -0.09 0.37 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.196 r_dihedral_angle_4_deg 15.441 r_dihedral_angle_3_deg 12.72 r_dihedral_angle_1_deg 5.756 r_sphericity_free 4.056 r_scangle_it 2.944 r_scbond_it 1.919 r_sphericity_bonded 1.785 r_angle_refined_deg 1.313 r_mcangle_it 1.229
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.196 r_dihedral_angle_4_deg 15.441 r_dihedral_angle_3_deg 12.72 r_dihedral_angle_1_deg 5.756 r_sphericity_free 4.056 r_scangle_it 2.944 r_scbond_it 1.919 r_sphericity_bonded 1.785 r_angle_refined_deg 1.313 r_mcangle_it 1.229 r_rigid_bond_restr 1.191 r_mcbond_it 0.797 r_nbtor_refined 0.309 r_nbd_refined 0.188 r_symmetry_vdw_refined 0.188 r_symmetry_hbond_refined 0.171 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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 3922 Nucleic Acid Atoms Solvent Atoms 562 Heterogen Atoms 20
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling