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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 3.05 59.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.241 α = 90 b = 104.959 β = 90 c = 181.038 γ = 90
Symmetry Space Group P 21 21 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 TOROIDAL FOCUSING MIRROR 2009-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 0.98010 NSLS X6A
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 3 50 100 0.271 7.6 7.3 23638 23638
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 3 3.11 99.9 0.851 0.851 1.8 7.2 2309
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 3HG3 3.04 49.63 22400 1128 99.52 0.216 0.214 0.2126 0.244 0.2405 RANDOM 34.52
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] -0.05 -0.06 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.025 r_dihedral_angle_3_deg 18.716 r_dihedral_angle_4_deg 15.836 r_dihedral_angle_1_deg 6 r_scangle_it 5.895 r_scbond_it 3.576 r_mcangle_it 2.768 r_mcbond_it 1.436 r_angle_refined_deg 1.413 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.025 r_dihedral_angle_3_deg 18.716 r_dihedral_angle_4_deg 15.836 r_dihedral_angle_1_deg 6 r_scangle_it 5.895 r_scbond_it 3.576 r_mcangle_it 2.768 r_mcbond_it 1.436 r_angle_refined_deg 1.413 r_chiral_restr 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6303 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 218
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction