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The structure of the bovine lysosomal a-mannosidase suggests a novel mechanism for low pH activation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HTY PDB ENTRY 1HTY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 PROTEIN 9 MG/ML IN 20 MM TRIS-CL, PH 7.5, 150 MM NACL MIXED 1:1 WITH 100 MM TRIS-CL, PH 7.5, 50 % SAT. (NH4)2SO4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.88 α = 90 b = 117.88 β = 90 c = 582.04 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 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.7 30 89 0.09 15.9 3 60071 51.3
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) 1 2.7 2.76 78 0.54 2.1
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 ENTRY 1HTY 2.7 30 60106 3071 89.4 0.257 0.257 0.2523 0.289 0.2475 RANDOM 38.8
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] 2.7 2.71 2.7 -5.4
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.4 c_scangle_it 9.9 c_mcangle_it 7.95 c_scbond_it 6.99 c_mcbond_it 5.12 c_angle_deg 1.5 c_improper_angle_d 1.11 c_bond_d 0.01 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.4 c_scangle_it 9.9 c_mcangle_it 7.95 c_scbond_it 6.99 c_mcbond_it 5.12 c_angle_deg 1.5 c_improper_angle_d 1.11 c_bond_d 0.01 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7124 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 222
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing