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Interconversion of Human Lysosomal Enzyme Specificities
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HG3 PDB ENTRY 3HG3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 PEG8000, Sodium Cacodylate, Magnesium Acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.1 60.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.947 α = 90 b = 139.492 β = 90 c = 182.58 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 FOCUSING MIRRORS 2009-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 1.07188 APS 24-ID-C
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 2.04 50 99.4 0.12 18.6 6.7 72009 72009
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.09 93.3 0.701 0.701 1.6 3.6 3354
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 3HG3 2.04 43.69 71961 3623 98.92 0.178 0.176 0.1841 0.218 0.2273 RANDOM 37.453
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] 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.82 r_dihedral_angle_4_deg 12.803 r_dihedral_angle_3_deg 12.129 r_scangle_it 9.8 r_scbond_it 7.455 r_dihedral_angle_1_deg 5.706 r_mcangle_it 4.839 r_mcbond_it 3.632 r_mcbond_other 1.526 r_angle_refined_deg 1.056
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.82 r_dihedral_angle_4_deg 12.803 r_dihedral_angle_3_deg 12.129 r_scangle_it 9.8 r_scbond_it 7.455 r_dihedral_angle_1_deg 5.706 r_mcangle_it 4.839 r_mcbond_it 3.632 r_mcbond_other 1.526 r_angle_refined_deg 1.056 r_angle_other_deg 0.964 r_chiral_restr 0.099 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6241 Nucleic Acid Atoms Solvent Atoms 559 Heterogen Atoms 257
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction