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Human lysosomal beta-hexosaminidase isoform B in complex with intermediate analogue NAG-thiazoline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NOU PDB ENTRY 1NOU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 5 mg/ml HexB [final], 50% saturated ammonium sulfate, 50 mM potassium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 3.19 61.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.414 α = 90 b = 112.414 β = 90 c = 397.232 γ = 120
Symmetry Space Group P 61 2 2
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 4 bent conical Si-mirror (Rh coating) 2001-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9 APS 14-BM-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 37 52315 -3
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1NOU 2.5 36.76 49713 2597 100 0.19964 0.1982 0.2021 0.22671 0.2037 RANDOM 24.379
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] 2.47 1.23 2.47 -3.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.192 r_dihedral_angle_1_deg 4.297 r_scangle_it 2.368 r_angle_refined_deg 1.557 r_scbond_it 1.492 r_angle_other_deg 1.175 r_mcangle_it 0.921 r_nbtor_other 0.48 r_mcbond_it 0.475 r_nbd_refined 0.181
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.192 r_dihedral_angle_1_deg 4.297 r_scangle_it 2.368 r_angle_refined_deg 1.557 r_scbond_it 1.492 r_angle_other_deg 1.175 r_mcangle_it 0.921 r_nbtor_other 0.48 r_mcbond_it 0.475 r_nbd_refined 0.181 r_xyhbond_nbd_refined 0.152 r_symmetry_vdw_other 0.147 r_symmetry_hbond_refined 0.147 r_nbd_other 0.142 r_symmetry_vdw_refined 0.124 r_chiral_restr 0.092 r_symmetry_hbond_other 0.073 r_xyhbond_nbd_other 0.066 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.003 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7756 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 107
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling