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Crystal Structure of human alpha-N-acetylgalactosaminidase, Complex with Galactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H53 PDB ENTRY 3H53
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.1 293 PEG3350, citric acid, Bis-Tris propane, pH 4.1, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.28 62.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.864 α = 90 b = 114.514 β = 96.17 c = 68.371 γ = 90
Symmetry Space Group C 1 2 1
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 210 TOROIDAL FOCUSING MIRROR 2008-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 0.979 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 1.9 50 95.8 0.117 10.1 3.7 87369 28.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 98.2 0.698 1.7 3.6 8937
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 3H53 1.91 28.57 87311 4397 95.29 0.198 0.196 0.1984 0.236 0.24 RANDOM 24.907
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] -0.09 -0.13 0.1 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.702 r_dihedral_angle_4_deg 17.166 r_dihedral_angle_3_deg 13.307 r_dihedral_angle_1_deg 5.584 r_scangle_it 4.619 r_mcangle_it 3.547 r_scbond_it 3.256 r_mcbond_it 2.496 r_angle_refined_deg 1.084 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.702 r_dihedral_angle_4_deg 17.166 r_dihedral_angle_3_deg 13.307 r_dihedral_angle_1_deg 5.584 r_scangle_it 4.619 r_mcangle_it 3.547 r_scbond_it 3.256 r_mcbond_it 2.496 r_angle_refined_deg 1.084 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6162 Nucleic Acid Atoms Solvent Atoms 896 Heterogen Atoms 311
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling