☰ Navigation Tabs
The Crystal Structure of beta-hexosaminidase B in complex with Pyrimethamine
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 50% ammonium sulfate, 50mM potassium phosphate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.94 58.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.898 α = 90 b = 113.898 β = 90 c = 397.427 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 MARMOSAIC 325 mm CCD 2008-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.8 35.9 92.1 0.174 14 8.1 35710 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.8 2.89 87.5 0.501 2.1 5.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 Isomorphous replacement THROUGHOUT PDB entry 1NOU 2.8 35.9 54068 33909 1801 92.2 0.197 0.194 0.2038 0.252 0.2534 RANDOM 43.01
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] 2.46 1.23 2.46 -3.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.021 r_dihedral_angle_4_deg 19.421 r_dihedral_angle_3_deg 18.324 r_dihedral_angle_1_deg 7.051 r_scangle_it 4.136 r_scbond_it 2.406 r_angle_refined_deg 1.882 r_mcangle_it 1.359 r_mcbond_it 0.662 r_chiral_restr 0.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.021 r_dihedral_angle_4_deg 19.421 r_dihedral_angle_3_deg 18.324 r_dihedral_angle_1_deg 7.051 r_scangle_it 4.136 r_scbond_it 2.406 r_angle_refined_deg 1.882 r_mcangle_it 1.359 r_mcbond_it 0.662 r_chiral_restr 0.115 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7750 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 176
Software Software Software Name Purpose Blu-Ice data collection CCP4 model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CCP4 phasing