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Crystal structure of beta-hexosaminidase from Paenibacillus sp. TS12
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 2.28 46.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.615 α = 90 b = 101.981 β = 90 c = 107.622 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 2006-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1 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 1.8 50 98.5 0.058 24.4 5.3 48251
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 1.8 1.83 91.9 0.148 7 3.6
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 1.8 27.52 45809 2431 98.51 0.138 0.13619 0.1361 0.17216 0.1722 RANDOM 11.183
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] -0.12 0.6 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.618 r_dihedral_angle_4_deg 16.154 r_dihedral_angle_3_deg 12.428 r_dihedral_angle_1_deg 5.656 r_sphericity_free 3.353 r_scangle_it 2.818 r_scbond_it 1.809 r_sphericity_bonded 1.657 r_angle_refined_deg 1.244 r_mcangle_it 1.173
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.618 r_dihedral_angle_4_deg 16.154 r_dihedral_angle_3_deg 12.428 r_dihedral_angle_1_deg 5.656 r_sphericity_free 3.353 r_scangle_it 2.818 r_scbond_it 1.809 r_sphericity_bonded 1.657 r_angle_refined_deg 1.244 r_mcangle_it 1.173 r_rigid_bond_restr 1.092 r_mcbond_it 0.739 r_nbtor_refined 0.307 r_nbd_refined 0.189 r_symmetry_vdw_refined 0.183 r_xyhbond_nbd_refined 0.136 r_symmetry_hbond_refined 0.131 r_chiral_restr 0.088 r_bond_refined_d 0.011 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 619 Heterogen Atoms 9
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling