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Crystal structure of beta-hexosaminidase from Paenibacillus sp. TS12 in complex with GlcNAc
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 2.27 45.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.328 α = 90 b = 101.734 β = 90 c = 107.818 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 ADSC QUANTUM 315 2006-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 1.6 50 99.4 0.143 15.2 6.9 68795
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 1.6 1.66 94.5 0.471 2.2 5.1
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 1.6 42.61 65282 3482 99.37 0.1507 0.14945 0.1495 0.17391 0.1739 RANDOM 12.143
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] -0.27 0.58 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.965 r_dihedral_angle_4_deg 15.486 r_dihedral_angle_3_deg 11.68 r_dihedral_angle_1_deg 5.913 r_sphericity_free 3.03 r_scangle_it 2.537 r_scbond_it 1.799 r_sphericity_bonded 1.714 r_rigid_bond_restr 1.269 r_angle_refined_deg 1.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.965 r_dihedral_angle_4_deg 15.486 r_dihedral_angle_3_deg 11.68 r_dihedral_angle_1_deg 5.913 r_sphericity_free 3.03 r_scangle_it 2.537 r_scbond_it 1.799 r_sphericity_bonded 1.714 r_rigid_bond_restr 1.269 r_angle_refined_deg 1.247 r_mcangle_it 1.094 r_mcbond_it 0.718 r_nbtor_refined 0.309 r_nbd_refined 0.191 r_symmetry_vdw_refined 0.16 r_symmetry_hbond_refined 0.129 r_xyhbond_nbd_refined 0.115 r_chiral_restr 0.085 r_bond_refined_d 0.009 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 3928 Nucleic Acid Atoms Solvent Atoms 620 Heterogen Atoms 20
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling